And the advertising, oh the random advertising. 
Probably the side-effect of an indie film
I loved the movie, but there were still some flaws that could've been worked out. The first one is the length and pace. Mega Man pretty much just owns the robot masters in less than 2 minutes, and while if they spent too much time on the fights, it may have ruined the movie, the problem still lies in that it's something that still should've been taken into account. The pace was also too long in other places, and just how it carries out over time. I understand you may need to pad a movie out for character development, but if you're going to do so, then don't let it drone on.
The second one was Dr. Light. He seemed (like Flame said) monotonous and dickish, but most of all, he seemed REALLY pretentious. He kinda seemed to put in more drama than what was needed, and seemed fond of using rather big words when they weren't needed. There's also the fact that his actions in the beginning seemed to justify Wily getting pissed off; he flat-out fires the man and during the interview he never bothers bringing him up that Wily helped out in such a big way, and at that point, all Wily REALLY wanted was just recognition and get a bit of fame and glory (and can you really blame him? They've just made technological marvels that may have just very well spat in the face of God and Wily just wants a "thank you" from the people).
Lastly, the sound effects. I understand that this isn't a Hollywood production, but there were many times I saw something going on but no sound, such as a fight with one of the Master Robots one of them would swing a punch and connect, but no sound whatsoever, no clanking or anything. At one point, the background music even just stops in the middle of a fight.