The enemies are simply too hard to kill and there aren't enough attack upgrades. I'm at 19 reputation and at least two missions are simply impossible with my current upgrades because a big enemy blocks the way, and my ship doesn't deal enough damage to take him down before I collide with him. I need more upgrades but all the available ones simply suck.
Vertical shooters should be all about the _attack upgrades_. Enemies should be dangerous but should also explode easily and you should have all different kinds of weapons to kill them. It sucks to have to pass enemies that you simply can't destroy, and it sucks to have a lame primary weapon that only shoots forward and does little damage.