You'll not break either one, so really your choice, all other things equal, is cosmetic. Anodizing is good, at least up front. It will probably resist the elements better. It will never polish up as much as a non-anodized version, though. On the flip side, once anodizing gets scratched or pitted, there's no fixing it. You'll just have to live with the marks. On a polished crank, a little fine steel wool/scotchbrite and/or wax/polish and you're as shiny as new.
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