That seems like a very sound approach and is how Hearthstone Battleground manages to have a large roster of units, but the player is still able to find synergies
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You could also consider this as an unlock feature after beating so many levels. That way you unlock more ways to play as you play the game, increasing replayability.
You might also be able to unlock a slightly different starting militia, for example. Imagine starting with 5 rats rather than 5 citizens. Or 5 skeletons. Or 5 laser frogs.
Yes! Different starting groups has been talked about and we are looking into that!
We are also doing more broad synergies to allow you to get out of tough spots when you need to...and also just to help keep the game exciting.
We are doing NextFest on Steam on the 19th of this month, that version will have more experimental updates, so be sure to check it out!