Some of these things seem like oversights (especially the grenade behavior) and if they're reported, there's a good chance that Nightdive will fix them; Doom 64 and Quake both received patches to fix things that weren't quite right with the engine changes they made, or at least they got "close enough."
Stuff like the chaingun windup/down, machinegun not pushing your aim upwards, and railgun damage were definitely intentional. I personally don't think the chaingun needed a buff, but I never understood the need for that bit on the machinegun. The railgun change seems like someone went "I don't understand why the damage values are different in multiplayer" and figured they were making enough other changes to single player things that they'd just wrap that in, as well; I wonder if that's a change Id intended to make at some point and just never did.
Intentional or not, I definitely echo Pho's want of a way to toggle things back to their original behaviors. Q2R is a large departure from how Nightdive handled D64 and Q1, and while there's clearly a lot of love for the game that went into it, the omission of a full "classic" gameplay option is definitely a thing to be addressed.
Either way, the reception to Quake 2 Remastered has been extremely positive, from what I've been seeing, and I think that's great. The game has been derided by a lot of the talking heads on the internet as slow and mediocre for much of the last 20 years, and it's nice that it's getting its day in the sun again.
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