Codex is a fine game indeed, but its a little over-designed IMO. I like the deckbuilding system in the game, and it really does feel like you’re playing an abstraction of an RTS game. However, I think it has a few too many rules (for example, the whole “heroes system”) that make it more complicated than it has to be.
To be honest though, I think many modern board games are over-designed in some way or another. Many designers (especially kickstarter game designers) just don’t cut enough chaff from their game systems.