Yeah don't go any higher than 2-3 in level for shields or 4-5 bars in engine until near the last 2-3 areas. Not worth it. You need to make sure you buy some extra crew as well as upgrade your doors to max to keep the enemy crew locked in. Another good thing to try is when they come on board, open the airlock and open doors leading up to where they are to deplete their oxygen.
Also, everyone should make sure they buy a Teleporter at some point along in the game, as early as possible is best. With the Teleporter, you just send your crew to their ship and take them out, leaving the ship intact and giving you higher rewards. It's also the best tactic for the final boss, since you can Teleport through the shields to take out the weapon systems without worrying about the weapons being repaired until the next stage.
- Xbox Tag: TheSweedishChef - NNID: Remni