I have to agree with Persona. Every palette doesn't have to be a reference to anything
But...but...MUH REFERENCEGURLS! D:
This one is a little complicated for me to have a definitive opinion on. Here's the thing: if the game simply must be shock full of references, I prefer when they stay within the alternate palettes as that feels like the least "intrusive" of choices.
As I said in other pastures and I think I'm amongst the vast minority in this matter, I believe Skullgirls' excessive amount of memetic humor and references are detrimental. I'm not opposed to the concept but in some instances it feels forced in the sense if offers nothing but reference for reference's sake that doesn't seem to suit the character nor the game world (I think Big Band's "My planet needs me." is a good example. I'm sure we all thought of that when seeing his winpose but it doesn't seem to fit the character at all.).
I can't say I'm a saint in that regard as I have made plenty of referential suggestions but they are, in my humble perspective, suitable for the character in a manner I feel won't make them act out of character and are not throw in for the sole purpose of memetic humor. Of course, all these things are highly subjective.
It doesn't detract my appreciation of the game or its characters but I do feel it's a aspect that chips away a bit of "professionalism" in its presentation, if that makes any sense. But this long winded ramble is of the game in general...
Concerning palettes, I only have one criteria to determine if I like it or not: does it look good? Doesn't matter if it's original or reference. I won't like a palette that stings the eyes or is completely unsuitable for the character just because "ohmigosh reference!"
In this matter it all boils down to case by case, IMHO. I love Parasoul's Megurine Luka and Kneesocks palettes simply because she looks amazing with those colors. Meanwhile, my favorite Bella palette is a original based off her bunny girl costume.