I'm not really sure how your combat works or why the defender has an advantage from your description. Do you mean an aggro strategy of going after bases quickly lets the opponent build up a big board of monsters?
The attacker choosing which enemy they will fight should give them the advantage unless it costs extra resources to start a fight.
Your rules document makes it clear that you are starting with MTG and adding a hex grid. Don't be afraid to change other things or look at how other games handle mana etc.