What do you mean by "some" poor mastering. Is there such a thing? It is either poorly mastered or well mastered. Mixing is a different story. Your song description is very long.
Here are my thoughts.
Is this a remix? Those arpeggio patterns have had their spotlight many years ago. Needs to be more original or at least put them in the background to accompany a more original lead pattern.
The bass at the very beginning of the song does not sound much different from a pre-sample. I'm not saying presets are bad to use, but usually presets sound poor quality so why would you want to use them?
I'm not really up to date with video game music, but I think I can figure where that megaman theme song comes in. Interesting idea to add your own stuff on with a video game song. At least you understand the idea what a legitimate remix is....some people just copy the original song exactly with the same instruments just changing a few frequencies here and there then calling it there "own" remix. I call that plagiarism. Anyway, nice job incorporating it in.
Critique goes to your drums. Really that's all you had? A simple kick and clap loops with changing hi hat patterns doesn't really count as innovative. And the reason why some may think your song is messy in some parts is because of the poor mixing. You have all your instruments all blaring out stereo. Where is the mono stereo? Where is the spreader or directional mixer? Where are the EQ variations? These are but a few things you can do to better mix your instruments. And no, you do not actually have many instruments playing at once so it is possible. Just combining 2 instruments in some parts of your song already sound messy so it isn't because the number of instruments you got going at once.
Lastly, I feel like you went crazy with the composition. This gives me the impression you just wanted to mash as many notes together to create a chaotic feel. Controlled chaos is good, not unorganized chaos.
I hope you don't see me being harsh on you. Its what I really feel. I don't waste my time writing long reviews without the intent of genuinely helping fellow artists get better. The one thing that is going good for you is that you have a knowledge about theory and staying in key with all the harmonies going. Being good at composition I find is a greater importance than how well you can use your music program....afterall the best dj/producers in the world have a music knowledge background (except deadmaus whom I am impressed with having a good ear). Overtime, you will get better with your music program and hopefully you will find that inspiration to make something unique. 5/5
bye for now