I don't think the alien origin is such a bad idea.
It's just that it created a lot of questions that went unanswered, mainly pertaining to Connor and Ramirez's memories of Zeist or lack thereof. Do immortals know they're from the planet Zeist from the moment they arrive on Earth? If so, why did none of the immortals in the original show no recollection of their alien origins? If not, when do immortals remember? Did Connor remember when he won the Prize in his battle with the Kurgan? If Connor has known since the end of the first movie, why did he never take the chance to return to Zeist?
I think they could have used the alien concept while not contradicting anything from the first movie so it's not inherently a bad idea. I'm sure they could have come up with something better, but the very concept isn't inherently offensive to me.
Other than the plot holes relating to Zeist, I feel that the movie focused too much on the Shield subplot. I understand that the idea is Connor used his new mind reading powers in order to help humanity, but it felt like the whole environmental message hijacked the movie in much the same way the arms race message of Superman IV hijacked that movie.