Okay, so I don't know if Amy will be in the movie or not, but recently, there was a storyboard from the movie that got leaked online. (We know the board is real because Paramount went out of their way to remove it from Twitter.) The board doesn't confirm or deny anything, but it does give me some thoughts about whether Amy's going to be in the film. Minor spoilers below.
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Spoiler
So, the scene shows Robotnik experiencing flashbacks (apparently) of events that took place earlier in the film. Sonic, Tails, Knuckles, Agent Stone, and Shadow all being seen at different moments.
But there's no Amy in the flashbacks. Or Rouge. Or any other new game character, for that matter.
Honestly, I think the fact that we haven't heard anything about Amy or Rouge being in the film (outside of maybe a post-credits scene) is confirmation enough. With the second film, they announced Knuckles was going to be in it way before the first trailer was out, in order to build hype.
Only other thing I can think of is that maybe the Knuckles series will have an Amy (or Rouge) tease at the end, and Paramount isn't revealing Amy because they want people to watch the Knuckles series.