I do notice a real difference in tonality between 35mm and 645. I somtimes show my portfolio on my iPhone, and even at those ridiculously small sizes, friends comment on the tonality in shots taken with my Bronica ETR (as opposed to the 35mm and digital work in my portfolio.)
Between your two choices, I suggest the Mamiya as a primary camera. Having owned and used a number of folders (AGFA Isolette, Zeiss Super Ikonta, Moskva5) I can't recommend any of them as your only camera. They are fun and can be quite handy (they fold after all!) I do get the occassional really nice shot from the folders, but I can't count on them to deliver the goods consistently. Things that conspire against getting a high rate of keepers include:
* a folding mechanism that means the lens and film plane aren't aligned to the same tolerances as a rigid camera
* often older, uncoated lenses
* focus issues exacerbated by a lack of rangefinder, or a rangefinder that is small or seperated from the main viewfinder
* often a small viewfinder window that makes composing more difficult
* shutter release ergonomics that invite camera shake
* big springs on faster shutters can induce shake in the lens/shutter unit (Moskva 5 :-)
My Super Ikonta fares the best of the folders I have, but I still only get about a 75% keeper rate (from a technical point of view.) My Bronica ETR however, will deliver 100% of the frames in focus with none of the issues that crop up on the folders. So important stuff gets shot on the Bronica, and I keep the folders for more casual fooling around. If a system camera like the Mamiya seems like too much bother, then I would suggest a TLR instead of a folder. A nice clean Yashica has none of the drawbacks of the folder and can be a real pleasure to shoot with. The results from my own Yashica LM have bested my Bronica and my Rollei 2.8F.
With regards to the difference between 6x6 and 645, it is a bit of a moot point. Especially if you print to the common rectangular sizes, you will be cropping your 6x6 negs to 645 anyway. The biggest difference between 6x6 and 645 is that the 6x6 camera doesn't need to be turned on it's side to change the orientation.