Anyway, I don't think Aliens wil be the antagonist of a Mario game for a while, so soon after the Shroobs.
If I remember correctly, the most recent non-spin-off Mario game released before PiT was PM:TTYD, which featured aliens (X-Nauts) as the antagonist. ...Assuming the moon counts as "alien," which who knows if they're even originally from there. So, it seems alien antagonists are becoming all the rage. XD
...I'm aware that SM64 DS was released in between those, but it's sort of a remake, so... Yeah.