Just like what Rolly Polly said, I don't want to ignore the amount of effort that was put into this. It's awesome to finally be able to play as Doomguy in SRB2, but there are a few issues I have with it that just make it really not fun to play as a DOOM fan.
The item drop system is extremely busted. Within 20 seconds of playing, I had already grabbed myself a rocket launcher, plasma rifle, and BFG before I even had a shotgun. It really doesn't seem balanced to be able to have an invlun sphere halfway through GFZ1 from killing a single Crawla.
It's a little funny to me how easy it is to get these OP weapons while you don't even have to use them, though. The BFG is usually great for taking out entire rooms of enemies, but due to the lack of tracers it's really just a slower rocket launcher. Speaking of which, both of these can kill Brak in less than three hits. I found myself playing through the game only occasionally shooting enemies with a pistol and saving my rockets for bosses. Unrelated to this, but the plasma rifle feels off to me.
I have a few more personal issues that are kind of stupid (such as the blinking animation, hud being different for no real reason, being able to look up and down, the chaingun actually shooting two bullets on clicking once when it's actually one bullet being fired and the sound effect being played twice, firing weapons not waking up enemies) but everything in the prior two paragraphs are my only real issues. I'd suggest watching decino's analysis videos on YouTube to help fix things like the BFG.
As for some of the issues you mentioned:
1.- The Item Drop system not being balanced is kind of a intencional, as there is 0 way to actually determine what kind of progress you are in campaing, singleplayer or co-op. A weak solution may be add randomized chances instead of literally all random.
2.- The BFG has tracers, the major problem is that SRB2 lacks any type of hitscan function since it got removed many years ago. So everything like the Pistol, Fist, Shotgun, Chaingun. Is just a hacked fast missile with Rail Ring's logic from SRB2's Ringslinger and there is no way to re-implement that other that STJr re-adding those functions.
3.- The Chaingun fire 2 bullets even with tapping the fire key once, the entire development of DoomGuy was based using the Doom's source code while finding a way to implement it into SRB2 itself.
4.- The HUD is different yes, but it's because things like keys display are worthless to implement as SRB2 removed that system already. As for the blinking, because it looks as a neat detail. That's all.
5.- About enemies waking up on firing, it's totally not ideal. Already talked about that with my playtesters, even if just a flood fill function to wake up enemies, going through all the map is just bad in performance as SRB2's maps are a lot bigger than Doom's map. And waking enemies is totally worthless too since enemies in SRB2 doesn't travel the map in long distances since it's practically impossible for them.
6.- And about looking up and/or down, Autoaim depends of thesse same hitscan functions that no longer exists. Simple.
After all, my goal for DoomGuy is just to have fun. Not to be critically 100% accurate, since already tried to do the most things possible with the limits of SRB2's engine.