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There are many API differences from polymaps that could be eliminated - getZoom() and setZoom(x) instead of just zoom() and zoom(x), etc. Personally, I find the polymaps API to be pretty solid and it'd be nice if one could swap out a lot of the functionality of the two toolkits without these more-nitpicky tweaks.
If you're writing libraries that can back onto either MM or polymaps it's trivial to write a compatibility layer, so I strongly disagree here.
I like the (admittedly java-esque) set/get routines, and badly miss verbs when in polymaps land. Much love to polymaps: I've learned a lot from it and it's extremely concise and elegant, but the overloaded getter/setters aren't free of overhead (conceptual or otherwise).
All right; this is low-priority. I'll axe for now.