With a chess timer, I'll be glad if my opponent upgrades Faeries, because it's simply not profitable. Considering that level 2 in Conflux is definitely not 50/50, but much lower, a choice between Faeries or Birds will arise very often. And this will only diversify tactics for Conflux and add extra interest to the game.
As for hero selection in Conflux, it can be handled like Necropolis. i.e., choose any hero except Luna (I hope everyone understands why), on all templates except Jebus Cross.
The fewer restrictions we impose on ourselves, the more interesting the game becomes.
That's my IMHO.