I understand what you mean, it's unfair but true: People appreciate original graphics in games more than is acceptable.
The main reason this is is that anyone can sit down and make a game with the RTP in a rather short time and it will be total shit. This makes people wary of games using the RTP because it is likely an indication of lack of effort, not to mention that (and I don't know why, as I personally love them) most people find the RTP chipset ugly.
However, if a game has original or, at the very least, non-standard chipsets, it makes it look like there was more effort put into it. I find this is just a silly way of fixing things that often doesn't fix the actual problem (as this is often the first thing people point out, it is often the first thing changed and the real issues remain).
So, if you think your game is good enough to stand on it's own, I wouldn't even worry about changing any of it graphically. Instead, work on the more important aspect, making your game fun and interesting on it's own respect through story and features.
On a related note... I really hope the whole game isn't like this boss battle because it would wear thin extremely quickly. You need to either go with RTP or try to rip (note, this does not mean rip off it means to extract them) graphics from final fantasy 6, but putting an FF6 graphic into the game just doesn't work for multiple reasons.