MGS3 is...different from MGS2, yeah. I'm of the opinion that the stealth gameplay of Snake Eater is better implemented than anything Sons of Liberty tried to do. Snake Eater actually felt like a stealth mission rather than any of the previous MGS games. Also, the bosses were a lot cooler than Sons of Liberty's. Snake Eater does get mindnumbingly boring at points though, due to the stealth aspect. There are literally hours that go by where all you do is hide from gaters. And the story is an ultimate wtf if I've ever seen one.
I'd still say give it a shot. It's my favorite MGS, despite its admittable flaws.