As you begin spending the cells you collect for upgrades (get that health potion!), the runs become more consistent, provided you're not rushing with reckless abandon.
I got to the first boss once, got them down to about 2/3 health before dying, probably could have beat him if I wasn't trying to sneak too many shots in each cycle.
I thought the framerate slowdown wasn't an issue until I hit one section I hadn't before (sorry, can't remember the name). Holy hell, it just came to a crawl and there were awful sorts of input delay that ended up hurting me so much that I gave up and let the game kill me. Has sort of turned me off to picking it back up until there's a patch to fix the issues.