Well, I can't really say why the AI in your game seems to love bombers. Because everything at Mk. I is pretty much a joke (with the notable exceptions of certain starships and recently, fortresses), frequently you will find that your first couple of unlocks are determined by what the AI chooses to use for that game. You had the unfortunate case where the AI loves bombers. In another game (such as playing a vicious raider) they will love ships that are immune to tractor beams, so you will need to invest in things that can slow ships down (such as gravity turrets and sniper turrets for their engine damage).
However, I will concede that bombers are disproportionately (read, to an unbalanced degree) the scariest of the triangle ships when used against a human player. The structural bonus of bomber like fleet ships most certainly needs a rebalance of some sort.
If you want more homogeneous waves, try settings the schizophrenic AI modifier in the lobby. The AI will then used mixed waves, instead of each wave being a single fleet ship type. It's a little sad that this is not the default, as it seems much smarter and is a lot more fun to fight. Sadly, you cannot apply that to a current game, you will need to restart the game to get this.
EDIT: Dang it, ninja'd badly on the scitzo settings suggestion. That's what I get when I don't refresh apparently.
EDIT2: WOOO!!! 100th POST!!!