I LOVED TA.
That being said, there were definitly areas that needed improvment, and I hope this game does them
For example, big units (like battleships) need to either be much faster to build, or (preferably) live much longer. It would take quite a while to build something like the battleship, and it would get sunk in a few seconds once in combat. Id like to see some big units that make a DIFFERENCE in battle, something that could really turn the tide. Like the Supercruisers in Homeworld 2. They took a long time to make, but once built they could really take a pounding. And when one arrived on the scene of a capship battle, you knew it was going to be a big factor. And don't say "wait TA had the Krogoth!" because that thing was never supposed to be built, especially not in multiplayer. The game designers basially said "yeah, well if your opponent is lax enough to actually let you build a Krogoth, they deserve whats comin to them."
The other weakness (I felt) was air units. They were expensive to build, and really didnt seem to be all that effective.