* Player speed increase/decrease
Very easy, in fact you have absolute control if you use SV_PlayerPhysics.
* Player classes with different starting weapons/abilities
Yea, there are lots of mods like this such as Team Fortress.
* Self recharging shield that can be used to boost damage, speed, weapon accuracy
Yup
* Crouching
Yes, darkplaces supports crouching -- Nexuiz uses it for example.
* Alternate firing
Yup
* Light amplifying vision mode
Hrm... this I don't know.
* Use button
Yes
* Scope
Like a sniper scope? Yea, Nexuiz has one, and I made one for my sniper rifle in Conquest.
* Distort model polygons, because some weapon hit the monster/player
You mean, change the model when the target gets hit? No, there isn't that ability atm.
* Some projectiles that stick to world and entities
Yup.
* Ability to move in walls and ceilings for players and monsters
Like moving right through the wall as if it's not there? Well, yes, but you have to be careful where they go in doing so. If you limit them to only going through certain walls that you specify, it'll be a lot better.
* Foot step sounds that interact with the world material
Yes, though I really recommend that you use textures with some kind of naming convention, such as "metal_<texturename>" for metal textures, "wood_<texturename>", etc. This will make it so you can just test what the prefix is to find out what kind of surface the player is walking on. The normal quake textures do not really consistently follow such a convention as far as I know.
* Monsters who help player
Yes, various mods like Archmage have done this. You can summon monster helpers, or have computer-controlled (though admittedly stupid) humans helping you out. I believe another person on the IRC chat rooms is doing monster summons as well, and I've done them myself.
If you have questions on
how to do these, just ask.

When my computer inevitably explodes and kills me, my cat inherits everything I own. He may be the only one capable of continuing my work.