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I don't think Nintendo will do a direct before E3 unless it's an 'E3 preview direct' which, if that were to happen would probably be a day before their presentation at E3 or so close to E3 that it wouldn't really matter.
I can't see Pokemon doing a direct before then either, I think they'll release any new info at E3 too. It might be uncharacteristic for Pokemon to do that, but I can't see them having a problem with it. It used to be that Pokemon announcements didn't happen at E3 because the younger Japanese crowd didn't watch it like the West does, but what with every announcement being mirrored to different language YouTube, twitter accounts etc. now anyway I don't think realistically there's any reason they wouldn't announce a game at E3.
If there's a Pokemon direct after E3 then anything shown is very unlikely to be releasing this year. It'd either be too soon after E3 that there'd be no point not showing it there or too long after E3 that there isn't enough time to hype the game before release.