I hate Thanos Attacks and it needs to die in a fire. It's got nothing to do with the progression of the game at all. It was crammed in because Gary Stern whined that players would never see Thanos if he was only the final mode. No, the points aren't worth risking a ball. It's way too many shots. I always select Soul Gem and just trap up and let him have it, then win it back later from Black Order MB or Battle Royale or Hawkeye.
Agree that Space Gem isn't useful enough. I always do it last. Moving the gems around doesn't really do anything, or actually it's usually a net loss, in moving gems to worse locations more often than to better locations (since you put them on good locations in the first place.) You can do cutesy stunts like the 2-flip Soul Gem, but that's way more work to set up than it's worth. It doesn't really work to use Space Gem to recharge Mind; it's not going to land on a powered-up avenger often, and an unpowered Mind isn't very useful.
Thor takes way too many hits after the first one. Seriously, 9 risky rebound shots for a 2-ball multi? I never go for that, unless I accidentally get multiple hits with the Widow inlane helper. Thor always gets completed from Spot Avenger after the first time.
But really, the game's problems aren't code related. Code can't fix an uncooperative Marvel ramp, or that every reject from the Hawkeye loop blasts straight down the left outlane, or that half the rebounds from the disc area go down the right one. What AIQ really needs is an outlane ball resurrect feature, like on Star Wars and Rush and Led Zep and many others. There's no insert on the playfield for it, but it could be indicated by flashing/pulsing the I or N outlane light.
The biggest thing code could fix is how many times you need to spin up the disc to enable the next mode. I drain half my balls just doing that. The game could really use some shortcut to spinning up the disc sometimes, maybe the Sanctum target. Also allow disc spins to count during the Collect Gem / Place Gem steps, it's completely maddening that you have to finish those before spins will count again. Also for Thanos Attacks, just enable it right away like the Assembled modes instead of spinning up the disc yet again, if you're going to screw over the player with this useless mode, at least give him that much.