Would making armor, weapons, and magic interact more complex add depth? With enough added complexity, can the game become "un-min-maxable" and thus more elegant?
Not really, because AI War accomplishes this by taking away some of the choices that Elemental gives players. Except for the Riot Control Starships, you don't customize ships in AI War. You research some (and research is so limited that it's impossible to get everything unless you are winning by so much that you don't need research to win), and use capturables in the form of limited advanced research stations & AI factories to unlock rarer stuff.
I can't decide that because the AI is using bulletproof fighters that I'm going to build ships with anti-fighter armor and laser gatling guns. In Elemental I CAN decide that, because I can customize my units. So long as I can do that you can't really get rid of min/maxing.
If we had one of the more complex economic models that were originally proposed for Elemental, then you could do more things because rersources for the rarer items would be limited and you might not have them. AI War does that with the Spirecraft in Light of the Spire: in some systems there's rare ores and you can use one to build a Spirecraft. They're a one time use only resource, and if your Spirecraft ship dies you have to take another system with more rare ore to replace it.
Finally, AI War's multiplayer is entirely coop and as such it can be a totally asymmetrical and somewhat random game in terms of what you can get access to without causing as many problems. Since they decided to focus on competitive play in Elemental for reasons that I have never been able to understand, that won't work as well.
Would forcing players in elemental to play with some more variety - IE, a couple random Sovereign traits, a couple random starting units/buildings, help make elemental more interesting?
No, it'd just make people reload more until they get what they want. AI War also lets the player choose their starting location and the enemy AIs to fight if they don't want to play it randomly.