The endings did suck, but not because they didn't make sense. It's because the multiple endings are pretty much exactly the same with minor differences, like a change of color scheme. Plus it offers absolutely no closure about your crew or how your decisions ended up affecting the universe. And if people were to draw their own conclusions based on what they learned from the previous games, then it means at worst, everyone pretty much died and whole worlds were destroyed, or at best all of the armada you gathered is going to be trapped on Earth for a long, long time. But it definitely didn't help that the final choices were vague and the ending itself made absolutely no sense to the point where people are saying it must've just been a dream.
When I heard about how horrible the ending was, I thought everyone was just being a bunch of whiners. Then I won, and I thought meh. That was stupid, but I didn't care. I thought it was dumb that crew magically teleported,. Then I tried a different ending it was the exact same thing pretty much. Then I youtubed the third ending because I didn't want to sit through 20 minutes of unskippable cutscenes and dialog again, and it was the same thing yet again. That doesn't seem like artistic vision to me. It seems like FU to the fans.