These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Broken Base: A genuine attempt at Capcom appeasing its fanbase? Or a half-assed attempt project to not outright ignore one of their biggest franchises' 25th Anniversary?
As is par for the course these days, Fan Dumb is not far behind—on both sides of the argument.
On another front, the question of which characters should represent Street Fighter is not without its fair share of bickering. While the line-up for the regular eight World Warriors is fairly balanced (even counting Ryu as a technical SFII vet, SFII only comprises half of the spots; the remaining three bosses and the True Final Boss are all from II, though), debates range from "Where's Bison/Akuma/Gill/Juri/etc.?" to "Alpha and/or III needs more reps" to "Still not a single soul from EX?" and just about everything else in-between.
Then there's the fact that it was originally a fan game that Capcom saw at EVO, which Capcom grabbed and touted as an anniversary game. Regardless of the game's quality, this has some fans pretty miffed.
Though the fact that they decided to endorse it instead of C&Ding it into oblivion like so many high-profile fangames have been in the past is at least commendable.
Not to mention Capcom of America are in a sticky position, seeing as how Capcom of Japan just doesn't seem to care about Mega Man anymore (if Rockman Xover, which is an obvious social game cash-in with almost no actual gameplay, is of any indication), and CoA have made it known they're just as miffed as the fanbase are. To actually go out of their way to officially promote a fan-game and let everyone play it for free is certainly a very nice gesture of goodwill. It's nice to know at least one side of Capcom actually cares about its fanbase.
There are some people who are upset that the one Mega Man game released in two years has Street Fighter in it.
The last gauntlet of bosses consists of Bison and his Devas/Grand Masters/whatever the translation is calling them now (with Akuma interrupting your match with Bison if you meet certain requirements), but Sagat, regardless of SF canon, is a no-show? Sagat has since been added to the game as of version 2, completing the Four Devas.
Demonic Spiders: There are many enemies in the game that can take loads of damage and have very annoying attack patterns. The teleporting guys that use Reverse Shrapnel in Dhalsim's stage come to mind.
Game Breaker: Optic Laser for the non-boss parts of each stage (against bosses that aren't weak against it doesn't do much more damage than a charged Mega Buster). It has enormously long range, top priority, and it KOs most enemies in one or two hits. Its only drawback is the higher ammo cost.
Good Bad Bugs: Certain levels can have E-Tanks out of place, which can help you get an extra one if you're lucky (and if they aren't stuck in a wall).
That One Boss: It would be a sin to have a Mega Man-related game without at least one of these.
Vega (Claw). He only uses melee attacks, but he's very fast and does a crapload of damage, and his weakness is a melee attack. He also has That One Attack where he leaps onto the railing and tries to slash down on you, and is very hard to evade if he performs it in the middle of the arena. In fact, the move you want him to use is his Limit Break, which isn't too difficult to evade and leaves him open in the center after it ends.
Akuma. At the start of the battle, he will instantly pull out his Raging Demon, which comes out extremely fast; if he successfully grabs you with it, you die. Rest of the fight he will usually spam fireballs, including really fast ones that travel through yours, is really fast and uses and often uses a faster version of Ryu's hurricane kick to move across the screen, during which you can't hurt him. Then again, this is to be expected from a Bonus Boss/True Final Boss. And Version 2 makes this fight even harder. How, you ask? If you use an E-Tank during the fight, it heals Akuma too.
Vega's stage is a huge pain in the ass. Half if it is one long vertical climb clogged with enemies, where one slip-up can send you falling down to the previous screen.
C. Viper's stage isn't too bad... until you reach the security system that starts blasting an instant kill laser behind you. If you delay to kill the barriers in front of you for even a second, the lasers will kill you just before you climb up the ladder to the next screen.