1. There should be another stage, Stage 4. On this stage the most powerful weapons of both sides will be unlocked.
Another stage would have to add a lot to the game and still be balanceable to be worth the effort of implementing it. Can you imagine being stuck at stage 1 because the other team got an early lead which allowed them to advance
three stages above you? That said I think we're all secretly pining for an Advanced Tyrant

2. A more effective version of the Egg and Telenode would be a Super Egg and Super Telenode. This is a group of three Eggs or Telenodes that saves space and build points. It would be unlocked at Stage 3.
I never see humans build more than two spawns, and aliens usually only do so for the creep benefits. Multiple spawns are usually made for insurance reasons more than to speed up spawning. A "multi-spawn" wouldn't really have any benefits over just reducing the cost of regular spawns, which itself doesn't add a whole lot to the game other than advancement for its own sake.
3. I recently saw the movie War of The Worlds and the weapon on the Tripods should have a place in Tremulous. That weapon would only have 3 shots but could take out a Tyrant in one shot. A downside would be that it takes a long time to reload. And, to be fair, you cannot refill the ammo for this weapon. It would be called the Quantum Destroyer (if you have another good name, I'd like to hear it) and would be unlocked in Stage 4 if possible.
I'm very much opposed to one-use expenses. If it needs to be nonrefillable in addition to having a slow reload and small ammo capacity than it's probably just overpowered (
four hundred damage in one hit?). I wouldn't mind seeing a Gloom-like rocket launcher in Tremulous, but making the alien team's strongest class vulnerable to one hit kills is cheap and smacks of rock-paper-scissors balance that Tremulous has carefully avoided for so long. I can definitely see the appeal of a ridiculously powerful weapon (in contrast to an Advanced Tyrant for instance) but there's probably a fairer way to do it.
4. In wall turrets and Acid Tubes would be great addition to a base. They have the same characteristics as the regular turrets and Acid Tubes but save space.
Not sure what you mean by "in wall" but Acid Tubes can already be built on walls and ceilings. The same thing for Turrets has been
discussed before; maybe Timbo's opinion has changed since then.
5. Thanks to Voodoo, this next idea is a stealth building. This would provide stealth camoflage around some of the human building. The downside is that it must be activated manually.
What do you mean by "activated manually"? Would someone have to stand there to keep it up, or would it just have to be turned on once by someone (in which case how is that different than how all structures are built?)? Would the cloak go down when a structure is damaged then have to be reactivated manually? Would structures still show up on alien radar?
6. I've always thought the Telsa Generators for the humans was too weak, so what about a laser? Such a weapon would be unlocked in Stage 4 if possible, cost 15 build points and requires a Defence Computer.
So why not just improve Teslas? I don't think making an identical-but-more-powerful structure really adds anything to the game. Maybe at stage 4 all structures could just be improved somehow.
7. A new evolution for the aliens, the Queen. Unlocked in Stage 4, this alien is immoble once you have evolved to it. It provides creep like an egg and an Overmind, but doesn't need any build points. The catch is that you can have only one on the field. Also, it acts as a portable Egg.
Er, so it's an egg that anyone can build but there can only be one in a map? It's immobile but... portable? What happens to the person that evolved into it? Are they stuck to the ground but still able to attack, and if so wouldn't that make them essentially defenseless anyway? I don't think this one was very well thought out

8. I know this one is a major exaggeration but this may be a good idea. Megaweapons for each side would be unlocked in Stage 4 and require 50 build points each. For the aliens is the Mega Acid Tube, which spreads acid all over the arena. For the humans, it is the Tactical Nuke which acts like the Mega Acid Tube.
Fifty build points is a heck of a lot; these would have to be more powerful than
six Acid Tubes or Turrets, and I don't see that being possible for a constant area-effect weapon. Maybe a similar effect could be achieved with an upgrade to the Overmind and Reactor. Would fit in with the "everything gets better at stage 4" theme.
9. The toned down Tyrant seriously made the aliens more vulnerable. Tyrants should have a new attack. If you remember the Ultralisk from Starcraft with the two blades, the new attack for the Tyrant would allow the Tyrant to use both claws at once. This attack would make up for the damage loss made from the 1.01 update.
The Tyrant was toned down for a very good reason, I don't see how just changing it back would be an improvement. In fact, as of now aliens win more games that end with both teams at stage 3 than humans do so this would really be a step in the wrong direction. Maybe a stage 4 Advanced Tyrant could be like the godly 1.0.0 Tyrant.
I hope I didn't come off sounding like an ass, or even discouraging, I just wanted to help you think critically about new ideas. And it bears repeating that I'm not the one making decisions so my opinion only goes so far. New ideas are always a good thing.