Put me on the side of "KoF makes more significant gameplay+character changes than SF". They've all had their defining BIG changes games (Such as SFIII series with it's parries and universal overheads, or KoF and it's striker-games), but on a whole, SNKP is much more open to change their characters very cores.
You can't play characters all the same in SF, between games (Like Makoto and Dudley in 3S VS SSFIV), but their moves, personality, and basic "niche" in the game stays primarily the same.
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Anywho, as far as KoF changing... I don't really feel that here. Not in a negative or worrying way, anyhow. I feel it's just evolving along a path that it's been taking potshots at for years.
You can see grassroots to much of XIII, in the games SNK has made since reforming into SNKP, or that they made near their "original" death. The storymode is similiar to the involved cinematics of the endings of KoF 2003 and XI. The pre-fight convos in Arcade mode are similiar to SvC Chaos's Convo system. The more exaggerated art style we have now started to rear it's head with the new characters in 2003, if not beforehand. Weighty console extra ideas were presented in the MI series, as well as a more complex story, and bonus costume parts for characters. Their quality of balance also started to show up strongly in the UM games.
KoF XIII is finally making me feel like SNKP is joining the current-gen development circle. Just took 5 or 6 years!

I think NGBC XBLA was a good early taste (with the widescreen game, color edit for online, redrawn portrait art, and freshly-created stages), but XIII is finally the real deal.
I always felt like I could hold a UM game up alongside a SFIV, or a BB, in terms of gameplay quality, and say "What I'm playing is just as good as what you're playing!" though the "didn't I see these same sprites in 96?" look and content of the game made this action little more than a sad cry for attention. XII didn't help this either; maybe if KoF XII was a PS3 / 360 launch game, it could have, but when it made it's way out, it wasn't even close.
But now we have *THAT* game that puts us on comparable ground. Not only does it have all the pros of other veteran fighter series, but it also has all the bells and whistles that come along with modern gaming. While "Solid fighitng Engine!" and "the ability to play it with a friend beside me, on my couch!" was enough for the older console / arcade games, people expect so much more now-a-days.
We're finally at a good spot with KoF now, for continued growth with the current consoles. Save for the fact that we DON'T know how the public will accept the game just yet, I feel incredibly positive towards everything they've done, so far.