The Flak Cannon is a replacement for both of Quakes shotguns. Itself a shogtun, but with a much wider horizontal spread than either of the base game weapons. This means it a much closer range weapon, certainly closer than the base Q1 shotgun, perhaps equal to the Super Shotgun, maybe a little closer. It tends to shine either at very close range, where few or no pellets miss and you have a strong chance of causing the enemy mob to flinch, or at slightly longer range against clusters of horizontally spaced enemies. In raw power it is definitely stronger than the Super Shotgun. For comparison it can kill a death knight in 3 shots, vs 5 for the SSG. Not only that, it takes 1 shell per shot and so is much more ammuntion efficient. It was very common in a lot of maps to be flooded with shotgun ammo at all times.
Finally, the FC's pellets bounce off walls up to 2 times. In tight areas this mitigates the larger horizontal spread a little, as the spillover pellets have a chance of still finding a target. It also opens up a few encounter and map design approaches. It can fire around corners to some degree with the bounce and there's almost certainly a few novel ideas out there involving hidden buttons and targets. My own map uses almost entirely shoot buttons to get around and being able to bounce off walls lets you hit buttons from places you wouldn't normally be able to reach, but only if you already know they're there, either by playing the map already or seeing the red glow.
In 1996 the grenade launcher came into this world perfect in almost every way and so is unchanged, bar some minor cosmetics around the way the projectile spins afaik. It does tie into the next new addition in an interesting (maybe problematic) way, however.
The MML replaces the Rocket launcher. Rather than firing a single strong projectile, it fires *8* smaller missiles in a row, with a modest reload before it can fire again. Each burst of 8 missiles costs only 4 rocket ammo however (this ammo is also still shared with, and so competitive with, the grenade launcher). Also notable is that you cannot cancel out of firing once you've started, self-damage is quite easy, both off terrain and off monsters that move in close to you.
This is a curious one. As far as I can tell the MML has a higher single target DPS than the grenade launcher. For comparison, the pretty tanky Amalgam (a new enemy) takes one volley of MML 8 rockets (i.e. 4 ammo) to kill. It also about double the time (but still 4 ammo) to do the same with a grenade launcher. In exchange, the MML seems to firstly have much weaker splash (or at least a much smaller radius). I've played a few hordish maps where I struggled using the MML on a large group of enemies before they could close on me, but the GL absolutely cleaned house once I tried that on the same groups. All this is great, the GL and Rocket Launcher in base quake were very much seperate weapons, but had a lot more role overlap than the Gl and MML do. MML for a burst of mostly single damage followed by a small vulnerable period, GL for more sustained output and bigger groups. I think the only spot where these 2 falter a touch is having a shared ammo pool. Because the MML takes 4 shots per volley, it feels extremely difficult to give enough ammo to run the MML and not also completely flood the player with GL ammo at the same time. This could be solved at a mapping level, maybe designing around only giving one to the player might be interesting? Still, its hardly a fatal flaw. I like this addition a lot. It fills a role that Q1 doesn't really have strongly, save the limited ammo thunderbolt of 'I need this one thing dead, pronto', but has a little twist the player has to manage
The Nail Gun/Super Nail Gun in base Quake are fine, but really long and widely recognised as being far too similar (the SNG is just an NG with faster ammo consumption and higher DPS). Some mods try and fix this directly (Copper makes the SNG far less accurate over long rangers), but QBJ3 opts to simply merge them. The result is an automatic projectile weapon with a fire rate somewhere between the NG/SNG. There's not a lot to add here, its a pretty strong all rounder, being usable at pretty much all ranges and limited mostly by chewing through ammo pretty quickly. A solid addition.
Another New Addition! This shares ammo with the new nail gun and fires large rebar spikes in a gentle arc (the metal bars that are put in concrete as reinforcement). These pierce through enemies, I think unlimited times, doing enough damage to kill all low tier enemies and do a chunk of damage to mid tiers. To compensate, it has a relatively slow reload animation, and a relatively (compared to the nail launcher) slow projectile. I suspect this is probably the highest skill weapon of the roster, making it quite unpredictable to plan around when mapping I think. It takes ten nails per shot, but that's quite an investment for something that in the hands of less skilled player is going miss quite a bit more and waste that ammo, and in the hands of a skilled player is going to save a lot of ammo over the nailgun by getting multiple kills or damage instances with it. Still, that kind of skill expression is appreciated, it values good movement, understanding how to lead your shots and having enough awareness to keep yourself safe during the vulnerable reload period. Really the main downside is Quake's sometimes slightly unpredictable movenment causing enemies to zigzag towards you unexpectedly and evade your shots, a similar feeling to when a single grunt ducks under your rocket in Q2, albeit less intentional.
The invoker is weird. Its a blood red arcane crystal that charges for about a second and a half, then emits 9 red beams that instantly kill any enemy in their path (it also leaves a blood red freeze frame of the enemies it kills in place that quickly fade out, I cannot stress enough how great it looks). It fills the Doom BFG spot that a lot of games like this have, a room clearer or very powerful weapon severely limited by ammo. It has a few issues though.
The melee weapon. As far as I know the functionality is mostly the same. Most of the change seems to be feedback. The Q1 axe is crap. It looks bad, it feels bad, its a weapon of last resort in a game where in the developer levels at least its pretty rare to ever run out of ammo. In contrast the wrench is much more smoothly animated, monsters are knocked back slightly when hit, and 2 monsters can be hit at the same time if you time it right. (I'm pretty sure that last one is a new feature, but I honestly have not used the axe for more than about 10 seconds combined through all of Quake I've ever played).
Its a better weapon all around. That said I have some reservations about making any weapon that has infinite ammo good, which I'll get too with the pistol. Its probably fine here though, it does take some skill to use (it looks awesome when you swipe a leaping Fiend out of the air too), is only close quarters and becomes a lot harder to use in more complex encounters.
The pistol is an infinite ammo (though it has a reload time every ten or so shots) short-midrange weapon that's pretty effective against small numbers of enemies.
I don't particularly like the pistol. In my mind the classic ID shooters are not a million miles away from Survival Horror games. There's little there for the player that a designer didn't place or intend to happen. They control pacing, mood and tone not just through encounter design and set dressing, but through powerup placement and ammo availability. The tone is different in Survival Horror of course, but that same tension of feeling like you might run out of ammo, while in reality enough has usually been placed for you to get by is the same. In Doom and Quake that designer hand is pretty strong. Melee can be ok in Doom, especially with a chainsaw or beserks, but it never dominates, partly because you can't punch things that are far away. In Quake meanwhile, melee feels so bad that the player would rather do anything else than skimp on shotgun shells with the axe. Other games swing away a little, Heretic handed a little control back to the player, allowing them to carry around powerups and use them at will. For an example completely swinging to the other end of the spectrum, New-Doom makes the player so self sufficient and their health and ammo pinballs up and down so often in a fight that designer placement of health and ammunition has little impact on the game. I like the former style much more, as a player and a mapper. I like being guided and controlled by the hand of a map designer, even when I'm not aware of it.
This is a very overwrought way to say that an infinite ammo weapon that's pretty effective at short-medium range is a problem for me. There are two possible scenarios. In the same way that the Rebar Cannon's skill ceiling means different players will spend different amounts of ammo in a more severe way than other weapons, having an infinite ammo weapon does the same. Not having a clear sense (or at least having a weaker sense) of how much ammunition the average player has means that one designer lever over the player experience is weakened just that much more.
The other argument against it is one of player behaviour. We all know that players will optimise the fun out of a game if given half a chance. Its very easy, especially when enemy numbers are low, to sit back and plink with the pistol at medium range. I think this is deeply unfun, Quake is a better game when you get closer and get stuck in. Melee enemies inherently need to close distance to do anything, and for various reasons ranged enemies drop off severely at higher than medium distances in Quake. As a result a weapon that is effective at medium range is very good. The nailgun also fills this role, but it does also have limited ammo. This kind of behaviour does exist to some degree in Q1. The base shotgun is low damage but surprisingly accurate at mid range, and it is often possible to sit back and slowly whittle enemies from a distance, but its still a less reliable thing than the pistol and does at least cost ammunition.
I think a better way of framing this problem though is thinking about what role the pistol is meant to have. As it is now it feels like it has 2 states. If not enough pressure is being applied to the player it becomes the de facto best option, it spends no resources and risks little but still feels good to use. If enough pressure is applied, the pistol becomes inviable, in which case, why does it exist? Neither of these feel great. I know I should use the FC at close range, I know I should use the MML against a single high priority target, I know I should use the NG at medium range. I don't see where the pistol fits in all of this.
With all that said... its fine, honestly. I have spent a lot of words complaining, but its not a fatal flaw. It is possible to remove the pistol at player spawn, which If I were mapping again I would probably would do. If some people really want to play in a boring way, fine. I don't love that it weakens the designers hand, but using the pistol as an occasional thing and as a clean up tool for larger encounters isn't going to turn the world inside out