Maybe think about how different enemies can cause the player to play differently and make good use of the weapon upgrades. If your enemies are all similar, the player will respond to them in a similar manner (shoot until dead). Some ideas to flesh out what I'm talking about:

1. Imagine a slow moving enemy that explodes when it dies. Maybe the player will try to get him in the middle of a crowd before killing him, causing a lot of collateral damage.
2. A melee enemy that can move faster than the player. This could make retreating / strafing difficult for the player. Maybe a weapon with an upgrade that slows or stuns an enemy temporarly would be fun!
3. An enemy that is highly armored.. An armor piercing upgrade could useful.
4. Small enemies that form swarms and are difficult to hit. Maybe an ‘area affect’ upgrade like exploding arrows would help.

@scott8 love it!