Looking at events and especially All Star, it's interesting that it's going to really hinder them going forward if they want to ensure DLC characters are included fully into the game.
It would appear Events have a limit of 8 on unique opponents. No event has more than 8 different opponents, and this even leads to awkward events where Doc, Sonic, etc have to be segregated into a random catch all "hey, these dudes were unlockable before!" despite Marth, Falco and Lucario, etc appearing in the normal game specific events. I imagine this is probably a memory restriction with loading the models in for the characters to spawn relatively quickly.
Since both the Melee and Past Secret Character events both have 8 opponents, it seems unlikely Mewtwo will be retroactively added to these events.
Further, with All Star, no era has more than 7 characters. Considering All Star, when possible, uses the 8 player versions of the stages, I'm inclined to believe the mode is modified from 8 player Smash for quick loading of characters and has the same 9 character limit events have (All Star supports 2 players, so it needs a max of 7). I imagine the 3DS even loads the 7 fighters into memory, or they take longer to spawn as the unload/load, I haven't really tested. It's also worth noting 1986 is split in two in All Star, with the Kid Icarus characters appearing in the era before it, the only instance where a year is in two different stages.
This leaves Mewtwo's era with an awkward 8 characters, which, depending on how All Star is loaded, might require some changes to how it's set up if it really is based on 8 player Smash (which seems actually able to handle 9 characters loaded into memory).
Going forward with more DLC, this may be even more challenging, as entire eras become too large and challenging for the player and as a result, challenges become more difficult and the game gets artificially longer. You get 2-3 DLC characters and they may need to add an entire new era to split stuff up more and throw another heart at you. Challenges that require you to not heal between rounds become harder and harder, to the point where it might be a very real issue. It'll also lop side All Star's difficulty to be middle heavy. Pretty much all of the request DLC characters (Wolf, Dixie, Squirtle, Krool) appear in the two 90s stages, meaning if they get in... the middle of All Star is going to be pretty bloated compared to the rest of it.
This may also somewhat explain the lack of Miis in the 2006 era. There just isn't the memory for 3 more slots in an already 7 person era. Maybe when they figure this out, they'll add Miis to All Star.
It'll be interesting to see if they go back and add Mewtwo to events and if he's in All Star. It'll be pretty lame if they don't, but there may actually be some technical reasons why they can't.
