I have mine all set up and because understanding the rules is really important to me, I took the glass off and set out to answer the questions about stackability and progression, etc. (Some would disagree with doing this, so, you know, spoiler alert.)
Here's what I found, and bear in mind that overall I think the game's a blast and it's understood there's code yet to come.
You can't start heroes or villains until you play Mags once, as Gambit reported. I found the lanes worked the same way he explained.
Wolverine multiball doesn't seem to exist yet or has some requirement that's not communicated. I couldn't start it no matter what I tried.
Stacking: basically, none. Once a mode is started, villain or hero, you can't make progress towards anything else except lanes and locking balls towards Mags. Hellfire hits don't count, character shots don't progress, etc. This goes for heroes, villains, and (I think) multiballs.
There isn't mode progression memory that I could find. If you start Cyclops and make three shots, you start over the next time. (And I'm not sure he's complete-able in the current code. It seems that it only registers shots after the spinner has come to rest first, which can't happen 9 times in the time given. Holding the ball right there and pushing it through, I couldn't complete it in time. Maybe other shots start to qualify, don't know.)
Starting all of the heroes, but not completing them, doesn't qualify the mini-wizard.
There you have it, all info subject to change, this is based on 20-30 mins of rolling the ball around with a rag in the trough.
(FWIW, I do like surprises, so I let most of the modes just time out and tried not to pay attention to the dots/requirements of each mode, focusing only on the stacking and progression questions.)
In my actual gameplay (relatively few games) I find that the ball is very trappable, the ball times are average, and actually completing modes is tough. It's difficult to light the lanes as many times as is required with the safest shot passing them over. Gonna have to dial in Xavier.