I don't agree that the Thalans should never use embassies, but it would be better if other strategies were more easily balanced with the pink blob of doom. As it is when I play with the Thalans they seem to be forced to use either laboratories or factories, which is more awkward than anything else. Making one or two super-planets on small maps is fun, but I don't like it that an entire civilization is so inflexible. Although it is probably too late to adjust for these changes, any balance that would include lowered research times for later laboratory or factory technologies. As for the embassies, you could just take out embassies for the Thalans. There would still be Cultural Exchange Centers in two technologies I think and the Thalans can always use extra diplomacy in the early game so that rushing those technologies would be no great loss. I enjoy the Thalans as a race because they play so differently from any other, and it is a bit annoying to have their strategies be either all ambassies(which I have tried and found interesting but would not want to use every time) or a restrictive infrastructure.
The races that probably could use help the most right now are those just below average races like the Arceans and Korx. It is rare to see these races be a real Galactic power, and whenever I see the Korx I start planning with the assumption that they will be one of the first races to be picked apart. This assumption has yet to fail in a number of matches, primarily small-abundant. The Arceans are better than the Korx for this, but whereas the Korx do something different from the other races(Evil diplomatic/ economic, trade in general as a powerful weapon) the Arceans are just dull to play. I have tried them, but just never enjoy them as much as other races. If I want to play with a militaristic strategy then the Korath, Drengin, Yor, or Torians are better options. For a more balanced strategy the Terrans, Iconians, or Korx are more interesting options (The Korx are fine with a human player, it is only really with an A.I. controller that the expansionist fodder criticism really applies).
Also, I am not sure if this problem has been fixed already, have not noticed it recently anyway, but when the Kryyn or Terrans refuse to build any ships at all the entire game. It is such a waste of a usually fairly powerful civilization when that happens. Overall, though, the A.I. seems to be much better so far than DA.
Edit: The solution to these issues does not have to be making the weaker civilizations stronger, any sort of subtle check to the early strength of the Torians or Yor or such would be acceptable, as you seem to be looking for smaller changes now.