The Dark Phoenix Saga
Days of Future Past
God Loves Man Kills
Age of Apocalypse
The Phalanx Covenant
E is for Extinction
Maybe both Messiah Complex and Second Coming, making it a Trilogy with a Third movie with AvX without the A getting in the way.
God Loves, Man Kills would very easily be the best choice for an animated feature. It would appeal to hardcore fans, as well as the casual viewer who is not all too familiar with the X-Men's vast and dense history.
All of those other options require that you are familiar with a large cast of characters, many Marvel Universe locations, and even years of established continuity. God Loves, Man Kills is conservative on cast and is distilled down to the real, core themes of the book: the bigotry and persecution of the different, and the choices in action the persecuted have. It does not involve aliens, alternate dimensions, alternate futures, or upending the status quo (E is for Extinction).
Call me crazy, but I always wanted to see an episode of The Wildways featuring Spiral, Mojo & Psylocke. :)
The trick would be finding an arc that could be told in 90 minutes or less, as for odd reason the studios think that the audience can not sit still for more than that. While it couldn't fit that criteria, I'd love to see the Asgard Adventures told New Mutants Special and UXM Annual #9, Acts of Vengeance arc, or even New Mutants Annual #2 done if they could capture the feel of the great art styles used in those. Realistically, they would probably have to do small character base stories and off the top of my head the Kitty Pryde and Wolverine mini-series would fit the bill.
Age Of Apocalypse
One of the most disappointing things about the cancelation of the Wolverine And The X-Men cartoon, is that the second season was gonna be the Age of Apocalypse . . . . . then it was canceled.
It still was truer to the source material than X-Men: TAS particularly bad adaptation of the Phalanx Covenant.
The real Phalanx Covenant, they still had humans killed in the thousands to make the Babel Spire. They didn't really get into that on the sanitized cartoon version. Or the awesome Generation X tale that should have been part of it.
I'd go with God Love, Man Kills. Its concise, has a limited cast, and exemplifies the core themes of the X-men mythos better than any other story. Besides, its one of the few arcs listed in the poll not adapted by the TAS already.
I don't mind them doing the recent stuff (Messiah Complex, Schism etc.) but I feel those arcs are way too convoluted and would only serve to confuse the casual viewer familiar to the X-men only from the movies and previous cartoons.
I would like to see an 'X-men First Class' styled DTV featuring the original team of Cyclops, Marvel Girl, Iceman, Beast and Angel.