Personally I think the airstrike beacon is a doable idea and in junction with an armor rush could somewhat even the odds for GDI.The nQ (n00b Quotient) idea isn't really implementable but **** would it be nice.
The Temple/CommCenter buildings would be incredible, but you'd invariably have people complaining about not having beacons when the other side does - though it's 5x harder for GDI to deploy a beacon than NOD.
The "Spy" character is a bad idea. Someone is already reporting "cross-team" characters (whether it's a cheat or bug is still up for debate), but the stink it caused is reason enough not to do it - besides - RA introduced the spy, not Renegade.
The IR goggles are definitely doable. Not by modders, but definitely by WW. Hell, the SP game has a PersBatSu with a scanner (in a cutscene - where mysteriously they just don't KILL Havoc - a la Austin Powers "I'm going to put them in an easily escapable position and hope everything goes according to plan...") that can detect stealth - so it wouldn't be TOO off the original story.
NEW IDEAS:
Some splash damage for the nuke. Not much, but hey, if you're gonna call something a "20 megaton hydrogen bomb," it shouldn't just take out one building. Either rename the thing to a tactical nuke, or make it lethal to any infantry in a set blast radius (not just the cloud) like it was in the game. A temporary radioactive zone wouldn't be too much to ask, either - and definitely doable - just code the area as a barren tiberium field with a rate of decay.
Personalized lines for different characters. I dunno about you, but a Hotwire/Sydney/Sakura saying in Havoc's voice "Keep 'em coming" is somewhat unsettling.
10 second reduction off a GDI beacon destruction time and 5 seconds off the deploy time. Face it, a geosynchronous satellite has a lesser "get up and go" time than a ballistic missile. Add the fact that it's very hard for GDI to be covert, and you make the sides a tad more even.
Server-settable limited superweapon beacons. Nothing is more annoying than a team doing nothing but laying beacons. If there were a minimum of five beacons for each side in the game (server settable), it would force SMARTER players to be much more sparing with them. And if you're on a team with a bunch of inbred idiots who waste them, well, you're screwed. That's life. If you ask me, you should only be able to buy a beacon if you're in the top 25\% of the players on the server - only elite players should be authorized to handle such destructive firepower.
Losing credits for FF kills. I don't know about everyone else, but if there's a PKer on my team, I don't want him wielding something which can give one-shot kills.
DEFINITELY a server-settable number of mines (max of 50-60), especially for servers with over 24 people.
That's all I can think of for now.