The flares may be gone, but the light they emit isn't. Kind of odd having those red lights with no source about. Sprite glitch in the second level still exists (where you can use one sprite to proceed instead of 6). Now would be a good time to patch it out at long last.
I didn't catch any other technical errors through my run of everything. I LOVED the Gauntlet arena though. You guys should totally add them into the spare slot in "random" depths in place of the one level that fits with the rest of the stratum. That is, make it able to chose between graveyard/TV/gauntlet wildcard arena (I'd expect them to change from the set families of the mission arena to two random families and a random status for each stage of the arena). It fits with the whole randomization thing, and would retain its novelty.
As someone with a fair amount of skill in the game, I can't really judge how the difficulty curve of everything is since I've plateaued. Makes me a bit useless as a playtester instead of a bugtester. I would like to see newbies urged to do Arcade runs at some point, though. They might just fall into grinding missions otherwise.