Rail gun isn't really a skill gun, especially instagib, I always found the real skill was with the lightning gun. pushing someone up a wall with it's amazing knockback was an art form. The main difference between quake, UT and TF2 is that old school everyone had the same weapons, no vampiric black box, no medic to keep you healthy, a lot of the game was centered around the red armour. and bunny hopping actually increased your speed quite considerably. But I digress..
My most hated class to play against is spy, closely followed by sniper, just because they usually kill you by utilising stealth, the sneaky bastards. I would however get rid of the medic first , closely followed by engy, or at least just ban sentries.
If you killed off spy, there would be less need for pyro to hang around nests so much, so could be utilised more in pushes, defense walls, etc. Also engy would become OP without spies.
Sniper could be killed off with no real down side.
I would like to see something like a ninja added as a 10th class, grappling hook, smoke bombs, camouflage and throwing stars, fast with huge jumps, but low initial health (~75hp).