I think that, on small maps at least, it is perfectly feasible to stop RA. The problem comes when you start playing longer games where everyone has had time to get higher fleet upkeep levels. The vasari player doesn't HAVE to rush to RA for it to be stupidly good. He can play normally, and then when everyone has lots of research and huge fleets, he has the ability to replace losses. With upkeep upwards of 50%, other people don't. The vasari player can take bigger risks with his fleet, accepting losses that would cripple TEC or Advent fleets. And it never stops, unless the TEC has somehow built a big fleet AND plenty of novaliths. Advent really has nothing to do.
They need to fix it in 1.04.
My two cents...
The fix can come in two parts. First, require that ships that come in have the requisite fleet research. Draw from all the ship types. A force of heavy cruisers will save you? Sorry, you get colonizers. Scuttle them, better luck next time. And, now you'll get the specialty cruisers like overseers and subverters. Much better.
That'll make it so that meaningful rushes are harder because it takes a lot of military labs as well as civilian. It won't stop the late-game dominance, though.
For that, I propose upkeep be a RANGE of percentages for each research level, a minumum and a maximum based on how many ships you actually have. Just pulling numbers out of the air, perhaps 0-10%, 5-20%, 15-35%, 30-55%, 50-80%...Hmmm...that's too much too fast, but you get the idea. The minumum of each level should be less than the previous maximum, so rebuilding is easier. This should make free fleets less of an insurmountable advantage in the late game.
With those changes, I think that the two times RA is truely overpowered will be curbed. It's too powerful at the beginning when fleets are small, and at the end when you have no money to build a new fleet because of the upkeep system's rigidity. During the middle, it's good, and a nice ability, but not game-breaking due to the cost of the research and stabilizers.
And that was way more than I wanted to write. I hope a dev sees it and it sparks some thoughts.