I have read your critique and have done a few changes, I have decided to stick with the DnB style and only remix the Sonic 3 boss in this style. I have also tried to clean up the mix a little.
However, I am finding this remix hard to add extra parts to, in terms of composition, as once you have remixed the two melodies inside the tune, there isn't much to do. I am currently experimenting with adding a section that sounds more like the 'mini-boss' part to flesh it out a bit.
Here's the updated drobox link:
Sonic 3 Boss ReMix, as yet untitled.
To maybe help those critique my work, I have added a Parametric EQ to the master channel to show the frequencies, this EQ doesn't change the output sound at all. The screenshot was taken at about 40 seconds in.
http://i.imgur.com/TeZ4dRo.jpg (It was a tad big)
Thanks again for the help.