Even if it has been a while, i still have some memories about Mario vs. Sonic.exe - sadly mostly bad ones. Therefore i was interested to see, if/how you improved in your remake.
You state that only 15% are done so far, so i'll just mention the roughest "flaws" (or what i'd personally define as flaw).
1.) First of all, your palette is still too red for me. It wasn't neccessarily eye-searing, but except for the castle level, aesthetically the levels were quite boring to look at due to being so monochromatic.
2.) The music in the 3rd level is quite unfitting imo. The level is "dark and scary", but the music is more "calm and pleasant". There are 2000+ ports in smwc's music section. I'm sure you could find something better.
3.) Using so many boo-rings in the castle level is a bit tiring, too (since oyu need to wait a lot). There's a boo-ring modification-tool on smwc (or sprite or patch, i don't know since i didn't use it so far). Perhaps you could create more interesting boo-rings, using that? Or you scratch them entirely and look for other sprites, which could be more interesting obstacles.
4.) Speaking about the castle-level: You should inform the player in advance that you need to collect 4 yoshi-coins there. Because if the player gets to the "control-blocks" and can't pass, he's forced to backtrack (which is anything but cool design)
These are the 4 main flaws i discovered. I hope i didn't sound too harsh, but if you want to improve, i want to give you the respective feedback, how you could actually improve this hack a lot (in my opinion). To say something positive though, i'm glad that you decided to work on this again and to remaster it. I just hope you are open to feedback, too, so this hack can be really
Good luck with it!