I was very fond of Metroid, back in ye' old days. Also of Megaman, but not AS much.
Either way, i like the way it turned out here. Besides running smoothly and without any problems(at least i found non) and creating the original feeling of both the games.(both terrain and enemy placement seem close to what the original would do).
And i especially liked that there's 2 paths to go. Had me go round past Samus first, to continue exploring, until i figured i'd already been there ;)
As for suggestions: Right now the selectable weapons do seem a bit...er..weak? They shoot in the same direction as your main one, have limited ammo, and there's nothing a charged up shot from your main won't kill. Either make the main not go through walls(while upgraded ones do) or have them shot a spread in 45 degrees upwards and downwards, too, or whatever :) but make them worth using...