That's a bizarre question, because you're really comparing a prosumer application (FCE) with a professional software suite (CS3 Master). FCE is somewhat limited in what video formats it supports. It'll do DV, HDV and AVCHD, but that's about it. You'll quickly find yourself wanting to upgrade if you need to edit footage that uses a professional codec, like P2-based Panasonic cameras.
Apple sells the educational version of FCS2 for $699. But my college bookstore had even better pricing on the same software ($499). I'd check with your college bookstore to see if they stock FCS2 and what they sell it for.
But with that said, there's still differences. For example, the CS3 Master Collection will give you applications like Photoshop, whereas FCS2 isn't bundled with image manipulation software.
In any case, you really need to choose the package that will suit your actual needs the best. I prefer Final Cut because I'm used to it. Adobe's equivalent is Premiere. I honestly can't comment on the current version because I haven't used Premiere in several years (and that was on a Windows machine). Both FCS2 and the Adobe CS3 family offer tight integration between individual applications.
What format of video do you see yourself editing the most? There are several standards (DV, HDV, DVCPRO, DVCAM, XDCAM, REDCODE, etc.).