I love a flat mouse, both for feel and for fitting in a travel bag.
I hate the big domed "shoe-mice" even as a I respect their ergonomics up to a point. But they take extra force: I have to move my whole arm, and drag the weight of my hand pressing down on the mouse's feet. No, thanks. I like a small mouse I can move with fingertips alone. Fingertips are more precise than my elbow! (In fact, when I use a domed mouse, I don't even bother resting my hand on it. I just cup my fingers higher and waste that ergonomic palm rest because it makes it hard to, you know, point at things.)
It's not at RSI issue because I use the best RSI-prevention of all: variety. Sometimes I use the mouse, sometimes the trackpad, sometimes a gaming mouse I keep on hand... sometimes even a big trackball. (And a lot of the time: an iPad!)
But I'd pick a Magic Mouse over a Logitech because I love Apple's scrolling mechanism. No wheel is good enough after trying that. I don't actually own a Magic Mouse because I'm waiting to get one bundled with a future Mac, but I love using them. (I also love the Magic Trackpad and might opt for that instead.)