I noticed a few things while playing the N64 campaign.
It's not 1:1 parity with the console version, and it's not meant to be (and that's a good thing, actually).
How it works is they use N64 textures, OST, and maps. Everything else is from the new engine - including the new enemy AI changes and balance adjustments, etc.
A good portion of the game is spent in anti-gravity. You may not have the rocket launcher, or much ammo for it yet, relying on grenades to take down bigger baddies like enforcers or tanks. The trajectory of a grenade on authentic hardware is net positive, so it's about impossible to aim. On Q2 Enhanced, it just means the grenade fires straight out of the barrel. Little things like that stand out.
The Nintendo 64 campaign on Hard, with deaths, took me about 3 hours. This is how I have always wanted to play this version of the game. It's indescribably better than trying to play it on an actual Nintendo 64 or even emulated.