Wasn't the vast majority of top 16 last year Trooper Spies? I don't recall last year being so diverse as you mention it to be. Either way, it's obviously not good PR for the game to only have one faction really represented. It's a tough nut to crack though. We don't want rock-paper-scissor either, so balancing all three factions equally seems like a tall order. With the coming wave and HotE though, it seems that Empire is getting the uniques they lacked - now that those are good enough to play and Rebels also get a small boost here and there. On top, we get the Droid cross-faction list.
I'm very hopeful that next year will see the best of the best of IA meta.
It's funny though, how many proclaimed the Weequays to be a useless version of HKs. I can see the merit to dissolving the Temp. Alliance cards, to break away from the Gideon/C-3PO in Merc. Merc could still get C-3PO - but would have to do it through the eJawa. Taking it down a notch. I'll predict that this will happen anyway though, as it saves you 1 point for a sweet upgrade or something similar and still gives you 2x Focus and C-3POs sweet Evade.