First of all, I want to say I'm a fan of this game, and I love the improvements done for version 2, but I think even more can be done still. Here are some ideas I had in mind.
1. At the end of Balrog's stage, you have the option of either walking over the collapsing bridge and letting Balrog fall to his death like normal, or jumping over the collapsing bridge and leaving it intact. If you do this, Balrog will make it across safely and then you actually get to fight him in an actual boss battle in front of the casino. This optional fight will also be the first step for unlocking a new boss in suggestion #3.
2. In the boss rush rooms of most other Mega Man games, a 9th teleporter appears after you kill the 8 bosses again, which takes you to Wily. Since the boss rush stage in SFxMM is Seth's Lab, maybe Seth could be added as the 9th boss.
3. Another True Final Boss, basically a second form of Akuma. There are four steps toward unlocking this boss, and all must be done without continuing. Step 1 is described in suggestion #1: Get a Perfect against Balrog the hard way (by actually fighting him as described in suggestion #1). Step 2: Unlock both of the other secret bosses, Sagat and Akuma, the methods of which are the same as in Version 2. Step 3: Get Perfect on both Sagat and Bison. (Bison's Perfect will count when Akuma drops from the sky.) Step 4: Beat Akuma (I'm not going to suggest the requirement of getting Perfect on him because it would just be too insane, especially since you can't abuse E-Tanks against him). If you did it all correctly, Akuma will not explode when he dies. Instead, he will fall to the ground and channel his Satsui no Hado energy to become Oni (from Super Street Fighter 4 Arcade Edition) and challenge you to the ultimate fight! If you die against Oni, you have to fight Akuma again, but he'll still turn into Oni after you kill him. If you get Game Over against Oni, however, you'll start back at Akuma, and he'll just explode like normal after you kill him this time.
4. An Achievement system, similar to Mega Man 9 and 10, with an associated ranking system.