I think Atropos is actually not that bad, except for this one move on its final form... It's the move where two of the green orbs go to the sides of the ship and follow you around and kick your butt mercilessly... Gets me every time.
You don't get enough money to begin with and all upgrades are rather expensive, and you don't get to keep them later on. And no offence, the jump from 600 to 1200 is just dumb.