Pro tips from my infinite knowledge of this game by having PARTIALLY SOLD MY SHIP...once...*cough*
Gain the most ore from farming bosses setup a fast attacking gun to one hit the boss for max money.
As far as I can tell there isn't a benefit from going past level 100 other then being able to sell your ship.
After level 100 focus on getting broken parts you can do this by destroying those green ships that appear on level 3/10 and 7/10. The fastest method I found is destroy all but one ship then backup and go forward one sector to kill the ships again.
For the first time selling your ship I recommend getting 25000-30000 broken parts. most upgrade cost 12000 for level one but I would recommend upgrading your drone which I believe go for 2000/4000/6000/8000 (I think.)
*bug* When you purchase the ability reset on the heavy mortar or activate the asteroid kitty. If you have skills on cooldown when you purchase the reset it locks in those cooldowns. So I bought the reset when my other skills were ready then when I reset my skills will be ready again infinitely. When I sold my ship the next time I bought the reset skill my cooldowns were at 460. When I press the reset skill button it will set the skill's cooldown back to 460 even if they were in the ready state.
Also please fix the cat asteroids. Having to click on them 10 or so times seems pointless unless you are trying to hide the fact they help out a lot. Also please don't spawn them in the lower part of the screen. Even when I am watching the game I am unable to click on them enough times before they disappear off screen.
Are the drones supposed to continue the quest when your offline?
As for a game...well I am still idling away so it must be good so far.