I'd also prefer alternating activations to the current set up. With that said, there's a lot of legacy built up around what kind of game this is. It'd be a core identity change involving (among other things) a real rethinking of how all the timings in the game worked.
However, there's a lot of mitigations available for the problems of whole-army activations. The balance team has shown a willingness lately to dole out interactive rules (Elara has Field Marshal:Retaliatory Strike, a couple people know Battle Charged which is group Counter-Charge). I would love to see more and more reactive stuff creep into the game.
I'm, as ever, very skeptical about the rampant imbalance and would for sure question the sorting mechanism that only judges units on how they interact with assassination. It just doesn't ring true- but I feel like the thread has got those in hand.