They probably won't have sentinels because they are trying to "keep it real". Granted the subject matter doesn't lend itself to this but 50 foot mutants killing robots are a bit of a leap. We can assume that X3 will focus on Pheonix and will have a slightly larger team consisting of Cyclops, Storm, Wolverine & Nightcrawler with Iceman, Collosus, and possibly Shadowcat acting as the "B" Team, getting into trouble and so forth.
On the badguy side, there no reason for Sinister to make an appearance. His motives for the most part are scientific, granted he's a sadist and slightly megalomaniacal about his work, but he doesn't come into direct conflict with the X-Men on a regular basis.
As for Apocalypse, he is so radically more powerful than any of the current de-powered roster, save possibly a berserk Storm, that they would have no way to beat him.
The most likely bad guy in X3 is D'ken, the Shi'ar emperor who seeks the power of the M'Kraan crystal to make him a god.
For those who haven't or don't read the comic, Operation: Zero Tolerance was the world wide response to Onslaught. Since the X-Men were the only ones left standing after the final battle it was assumed that they were the perpetrators of the loss of the rest of the heroes.
