I don't see any situation where the options would be 1080p no AA vs 720 or even 900p with AA. Not with cheap post process AA being available. And while I hope that forward+ renderers become more popular (yay for The Order 1886) most engines today use differed so MSAA is just too expensive for most cases even at 720p to be worth it so there is no 4X AA. There are so many different approaches to AA available to developers all with pretty different results.
Another variable is the upscale it's self, there is more than one way to upscale a cat. And they are not all equal by a long shot. Different methods can lead to very different results. Check out this thread for examples http://www.avsforum.com/t/1477339/so-youve-built-your-htpc-now-what-is-next-how-to-get-the-ultimate-picture-and-sound-quality-from-your-htpc-madvr-svp-xbmc-mediabrowser-jriver .
There really is not cut and dry answer to this question. There are a lot of variables that can have a big impact on IQ outside of resolution, visual style, upscaling, AA method, other post processing, type of renderer etc. Tho as a PC gamer I will always go for native res (or higher) I think there could be a place for reducing resolution to focus on greater pixel control for the developers as discussed here http://www.gamesindustry.biz/articles/digitalfoundry-tech-focus-does-pixel-count-matter?page=1 by people much smarter than I am.
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