Now quickly Googling balance and sins rebellion brought rather.. disturbing news that underlined worries I got when playing vs the AI.
Sins goes through periods of varying degrees of imbalance... honestly as far as faction balance is concerned I think its one of the best balanced in Sins history, which is impressive given all the stuff the expansions have been adding. However when Rebellion was first released it was pretty bad, so if you're reading older threads that probably explains that.
Yes there is still some concern about the Vasari, though they are infinitely more balanced than they were a year ago. Their ridiculous new Rebellion capacities are now at a more balanced level, its just their long standing late game tech advantages like phase gates and phase missiles that keep them in the number 1 spot. In the days of the original Sins this did not matter as much, since the Vasari had very severe early game disadvantages, so they were very much a race that was awesome if you survived but you were likely to die early. However, things like buffed Vasari capitalships and early offensive starbases and even quick start have made it far easier for competent Vasari players to survive until the late game, so there is not as much risk to playing them as there used to be.
The only reason Advent is considered the weakest is also because Vasari phase missiles hit heavily shielded units, like all the Advent's ships, much harder than anyone else. If someone made a mod where phase missile techs just increased damage instead of shield bypass chance I think the three races would be very close to each other indeed.