Dang, I don't know. I'm a big Metroid fan myself, but I also love DKC. I know if I had been a Snes fanboy as a kid, I'd be a much bigger DKC fan today.
One one hand, I would much rather have new main characters (from unrepped IPs) over villains/sidekicks.... But back to the matter at hand...
It's hard to choose. I like K.Rool being a goofy villain. Nintendo has always been about this type of characters.
However, Nintendo kind of botched up Metroid's anniversary not so long ago... And I do think they owe us Metroid fans something.
Donkey Kong is almost as popular as ever now, and Tropical Freeze tells me another DK rep is almost inevitable.
Meanwhile Metroid is kind of up in the air. Prime isn't popular in Japan, and Other M is hated almost universally (yeah it wasn't AS good, but it's not the trainwreck everyone makes it out to be).
It all comes down to this: Both villains deserve to be in. K.Rook would have a very fun moveset to play with. But Metroid, while nowhere near a doomed franchise, still needs a little spark of life. And Ridley in SSB4 would be a good start.
Who would I choose?
Ridley, to make it up to the fans of Japan (Prime) the West (Other M) and the World (Anniversary botch).
I just think METROID needs this more than DK does.
(But in the end, neither are in my top 10 so what do I know. XD)