Hmm, I'd probably be wary of both. I like Kaep more, I'm bearish on RGIII at this point.
There's a lot of potential change for both though.
RGIII is getting a new GM in Scot McCloughan, and Gruden and Scot will likely decide RGIII's near term future. That may or may not involve him starting.
Kaep, similarly, is getting a new HC, and we won't be able to guess how that will go until we know who it is, and even then it's speculation at best. For example, current defensive coordinator Vic Fangio will probably get different results from Kaepernick than say, Mike Shanahan (especially if his son, who recently left the Browns, follows him as OC).
My initial thoughts are that, no, Kaepernick will not be a bigger bust than RGIII next season, because Kaepernick does not have any direct competition for his spot at this time. If SF goes out and drafts a QB, or brings someone in to compete in FA, then bets are off, but atm, I'd say Kaep is safe for at least a little this season.
Though in terms of fantasy he's still probably just a QB2 at this point. That's not as far of a drop as RGIII's fantasy value had, but it's still a drop.