First off, let me say that this is a really big project, and it's probably not going to look like Capcom's level of quality. They have several people (probably 30 or more) working on any game (just look at the credits for MegaMan 10).
With that being said, I still think you should try to do it, because you will learn a lot from it. Anyway, on to some critique...
You have alot of things here, but overall, your pixels suffer from jagged lines, anatomy and proportion issues, and banding.
I'm going to assume you're going to borrow some graphics from Capcom themselves.
The Castle. It looks like you edited one of Capcom's castles, keeping the skull and the satellite dish with minor changes, and then adding the big "fangs" and the weird hypno-dish. From a design and architectural view, these things don't seem to serve any function nor aesthetic. It doesn't really add much to a castle. A good study of buildings, from real ones to crazy artsy ones to ones in comic book and other Capcom castles, from a design perspective, you need to add features that are both functional and aesthetically pleasing.
MegaMan/Protoman. They have significant perspective and anatomy problems, in addition to poor color choices, banding, and jagged lines. Especially the feet. Again, the best way is to study anatomy, from real people, to cartoons, comics, and other MegaMan titles.
The City. It looks good for the most part, except the clouds and the "tube" in the lower half. Although I think this was a direct rip from other titles...
Generally, you need to study art, and pixel techniques. If you don't understand what jagged lines or banding are, there are great topics on here you can search for. For anatomy/architectural/color choices....unfortunately, that comes from study, study, study, and practice, practice, practice.
I hope I wasn't too harsh on you. But if you really want this to look like a MegaMan game, I should tell you the truth.
And now cute smileys.
