<p>My son's interviewer asked why he didn't apply EA. My son told him he didn't apply to Harvard because they only had single choice (last year obviously) and he thought he was a better fit at MIT. The interviewer then spent some time trying to sell my son on science at Harvard. :) In the end Harvard still accepted him, MIT didn't, and he ended up deciding for Computer Science Carnegie Mellon was a better place for him.</p>
<p>Anyway, it's certainly not counted against you. (Especially now that there's really no reason not to apply somewhere else early.) If they like you, they'll take you.</p>