-The city shields are awesome using it like a guardian is a kick ass tactic, but having the travel speed at 6000 is abit much, it is a city. I moved it down 2000 for my purposes.
I'm not sure what you're referring to as "travel speed 6000". The Atlantis has a MaxSpeedLinear of 300, which is considerably slower than most capital class ships. And yes, the expanded city shields really do kick ass, hehe. Especially when it's leveled up and you have shield upgrades to boot.
-With most of the ships costing so much there is nothing cheap to leave home as defender frigates against heavy threats as it usually takes alot of time go back and defend whilst trying to be on the offense. Dont know if i said that right, but i think its in order for a few smaller frigates that cheaper to stay home and defend. (keep in mind the expansion might provide this role nicely with stations and what not)
The premise behind the ancients is fewer but far more powerful (and costly) ships. You can get destroyers fairly quickly (Tech 1) but you aren't going to have a lot of ships really fast. If you are concerned about rushes though, there is a small, cheap light frigate that can be built very quickly. It is extremely slow to travel between planets without a space gate though and is intended for local planet defense primarily. The Corsair frigate is a little cheaper than the cruisers and requires no research to access either. You are right about having your ships spread out and travel speeds, but that is where the Space Gates come in. Like Vasari Phase Stabilizers, they allow travel between any two planets directly but do so at almost instantaneous speeds.
-The "cruiser" class for atlantians are very pricey albeit powerfull almost too pricey to make them usable during your average game. I adjusted them in price and power to make them more afforable and in my eyes, playable.
It does take some time to get a sizable fleet going, there is no denying that. I haven't had any major troubles so far in my games though. I can usually get a destroyer out within a few minutes of game start and if you were really in a rush there are the light frigate class ships which are available right of the bat. I generally balanced the costs/slot count against the other races heavy battle frigates when I did the balancing. I am not going to claim that it is right on the money but I tend to play against multiple unteamed hard AIs in my private games and haven't run into too many problems early game. If anything, I tend to find that it's easy for me to overexpand in the early game as I tend to rush an Atlantis (about 5 minutes) which is almost unstoppable early on but only capable of acting as a single choke point. I tend to play larger maps though.
Feel free to modify the balance as you see fit for your personal use. I actually think, if anything, the Ancients are perhaps a little overpowered as they stand right now, though somewhat vulnerable early game if they aren't careful. We all have different play styles though, so I may not be seeing quite the same issues as you have so far. For my part, I have trouble bringing myself to play the standard races anymore, as I just prefer the playstyle I get with the Ancients.
I spent some time revisiting the Wraith mod I had started a while back and now have it up and running under 1.1 as well. It's definitely not complete but it is playable. I don't have a lot of time for modding anymore but I may possibly look at getting a more complete build of them done up and possibly releasing them as well. They also have fairly powerful cruisers, but to a lesser extent and might be more along the lines of the balance you're talking about. I'm not sure how the Stargate Invasion guys will like me doing so though, at one point the Wraith were being created in tandem to their Full Conversion mod. I know I'd love to do an Asgard mod as well, as I have some ideas for them already too but one project at a time...