Yes.
My main metric to see if sides are different in a game is: Do I need to change my tactics or strategy depending on the side I'm currently fighting? If the answer is 'no', then the sides are too similar.
I can understand why the devs did this, however:
1) If you learn one race, you can also play well with the other two (once you figure out bit of the tech tree)
2) It should be easier to competitively balance three similar races against each other, as you only need to worry about if type A counters type B. When all sides have types A and B you'll probably have less balance problems
3) Subtle differences are the 'perks' for choosing each race; since the races function roughly the same, players can gravitate to the subtle differences they like more: Economic advantages of the TEC, phase missiles of the vasari, etc.
Still, in a huge game like sins, the samey sides bother me: Here are three fleshed out sides with very different lore, yet they have the exact same ship types and different, but overall mediocre abilities? The lore does not affect the game, as the philosophy of the lore isn't strongly translated into the gameplay of the three sides. The look of the ships between the sides suggests that they would operate very differently, yet they don't, which is frustrating.
With three different sides, the number of matchups you can have as an individual race are three: your same race, and the two others. With each of the races playing differently, and needing to learn different strategies to counter the others, you end up with nine different playing styles or strategies that players must adopt. If the sides are identical, you simply have one strategy: counter the same technology, units, and strategies in any of the other players that you have yourself.
One overall strategy is far less interesting than the potential nine that this game could have. When a game this rich has the potential to have much richer combinations and relationships, samey sides are disappointing.
Of course, I'd rather have the game come out on time and be balanced with three samey sides, than have three unbalanced, potentially buggy sides in the release build, so props to the devs for choosing their battles