Something tells me that the Raphael in PM is different than the Raphael in YI (Related, but NOT the same.) ... I believe this because, after to beat Raphael in YI, he becomes a constellation (Of one star, heh) somehow. How can he suddenly go back to Lavalava Island afterwards?
As for the other island issue, I duly believe, like many of you have said, that there is a large archipelago (... FINE! Island chain.) where the species of Yoshies live.... Yoshi's Island being the largest and most well known. Lavalava Island and Delfino Island are others. (I used this idea to create about 3 more islands in the only Mario fanfic I've ever written.)
Yo'ster Isle is more than likely a mere vacation spot; None of the Yoshies actually live there, I don't think. That, and it can also be used as a gambling facility. Think of it as one of those hotel/casino deals in the real world.
Of course, there's the pressing question of why there's a large bridge connecting Yoshi's island to the Donuts Plains in SMW, but not in YI. And is the bridge still there now? And how would someone undertake such a large project? Yoshi's Island must not be too far from the mainland at all.
Meh, that was a lot of rambling about nothing.
Everyone has their own opinions, no matter how WRONG they are.