That's not really a spoiler. Its been known before the movie came out that the enemies in the movie were going to be aliens. They're even shown in the movie trailers. At least I think that's what those flying metallic cone things were. But apart from that I kind of spoiled it for myself by reading the article on Gundam wikia. It kind of takes an Ender's Game type turn regarding the aliens. That's actually kind of a spoiler if you can figure out what I mean. The movie definitely finishes 00 for good though.
But really though, out of all the series to have aliens, I think UC would've been better, since its been around for so long, and they're so far into space expansion. And come on, it's UC, what more can you possibly do? Another spacenoid rebellion? In 00, you have people who are still in the AD calender, haven't moved into space colonies (I know some exist, but its not as widespread as in the other Gundams), and yet they have a major encounter with aliens already.
And I don't think anyone has anything against Macross, so you don't have to worry.