Well it turns out that Emacs' heavy reliance on the control key is explained by the "Lisp keyboards" of the 80s, which influenced its early development. Control is next to the spacebar, where you can hit it with your thumbs.
I spend about half my day on Macbook Pro docked with a Windows keyboard, the other half using the laptop keyboard on the go. The modifier keys are crazily different, but luckily System Preferences > Keyboard > Modifier Keys lets you pick different mappings for your different keyboards. So I've been trying to get used to this setup:
Whichever key is next to the space bar is now Control, next comes Alt (Meta), and furthest is Super/Command/Windows. CapsLock is an extra Control key, for good measure.
Outside of Emacs, it's going to take some getting used to -- esp. Cmd-C/V, Cmd-Space, Cmd-Tab, the combos I use all the time on the Mac. On the plus side, copy and paste is more compatible with Windows/Linux key combos for copy/paste, where I was already used to "Ctrl-C" with a pinky.
Inside Emacs, using the thumb for Control feels a whole lot better. Control-X O, Control-X G, etc -- I use those constantly, and the thumb just works a lot better. I recommend it!