Having an Atlantis is pretty much game over for the other guys. 30,000 shields, plus 100% expansion, plus once you tech up and/or level it, it pretty much owns. Remember, it counts a free capital, and needing to do some relatively cheap research doesn't really compensate. Maybe up the research to tier 4/5?
Yes, it's powerful but it's not as indestructible as you might think. I'm pretty sure that a pack of equivalent fleet supply Light Frigates gives it a run for it's money in the early game - and don't forget that at 300 fleet supply you aren't likely to have much else for ships. Late game, yes the shield expansion is really good but I've had AI fleets take it down. It is especially vulnerable to anything that ignores shields... Phase bombers are it's bane and you had better have a backup plan if you're facing the Vasari. The only time you can get away with using the Atlantis with a lot of other ships (where it's shield expansion really shines) is either later in the game or if you are fortunate to only have to defend a single front (hardly ever the case).
I suppose if you rush built an Atlantis and drove it right at the enemy homeworld you would probably be able to take it out. At the same time though, if he just built light frigates and rushed you right of the bat, chances are he'd find you largely defenseless before you got the Atlantis out. He wouldn't even need nearly an equivalent fleet (in supply) in that scenario.
I know the big numbers seem crazy but an equivalent fleet supply of 25 Advent Heavy Cruisers do enough damage (at 65% shield mitigation) to take down a 30k shield in 180 seconds. Meanwhile, they comprise a total of 19,375 hull points and 20,625 shield points without any tech upgrades. I suspect the Atlantis would win because of it's drone swarms and attrition on the Destras but not without taking some serious punishment. 60 Cobalts by contrast would do 30k (at 65% mitigation) in about 155 seconds and comprise 36,000 hull points and 21,000 shield points (no upgrades). If memory serves me right, I have had to retreat my Atlantis when going up against a fleet of 40-50 light frigates with an enemy capital ship escort. I've had an Atlantis explode on more than one occassion when I thought I'd be fine and didn't pay close enough attention, and the loss is devastating (I usually reload, heh).
The free cap thing does muck things up a bit but diverts a big chunk of your early resources towards it and sets you back in early colonizing in time and variety (your not going to get volcanics or ice planets nearly as quickly). That's actually how I prefer to start when I play the Ancients so I'm familiar with the scenario.
I'm sure the balance isn't perfect but I did at least do some number crunching when I last tweaked things and while there are some issues yet, I don't think it's too far out.