Not bad
I can see you put a decent amount of effort in this, from the drawings to the attempts at humor and the conversations between the characters. Overall, I think it was pretty decent animation; not bad, but not great however.
To begin, let us start with the story and dialogue. The alien abduction scenario at the beginning was cliché- so many movies and cartoons start with that sequence or something similar. It didn't keep my attention and I found it uninteresting. You could have possibly done more to make it interesting- perhaps introduced the abduction in a different way rather than a flying saucer - pretty generic. (I don't know if I can say that this was justified at the end of the film since the animation made it evident that it was a time machine rather than a flying saucer- but I suppose that makes it more of an acceptable, albeit boring, introduction). The dialogue at the beginning was laughably stale: "Yeah, okay. Uh huh yeah yeah okay so so yeah so yeah..." "Alright cool", followed up by "Dammit that was my car." This boring dialogue just made your character so uninteresting. This in not excusable as you have a character driven plot and the boy had no depth or anything interesting qualities about him. The medieval girl was more interesting as you showed the viewers exactly what life was like for her, how she had to be cautious and worried about eating a turnip- that gets viewers involved and connected with the character. The final character was moderately developed, you made his personality show through with his dry, unchanging tone. The conversation the boy and the alien had though was not successful; you were relying too heavily on repetition of an unfunny back and forth joke/conversation between the two characters. All in all, for an animation focused more on story and dialogue to reach an incredibly unsuccessful punchline, this was only passable. Not bad, but definitely not good.
In terms of art and animation, this animation was lacking in strong drawings and decent movement. From the beginning, it was evident you made the decision to puppet and tween the majority of the animation in your movie. Since you omitted the actual frame by frame animation to help portray any character emotion, it would be assumed you put actual more effort into the fluidity of the tweening. However, the motion-tweening was minimal, non-fluid and incredibly boring to watch. It might have been improved if you spent more time on the art, which was very lackluster and looked like minimal effort was put into drawing. Having stronger drawings and form would have made the tweening more successful but you chose not to do that. Also gradients are hideous, the title screen was not not fun to look at at all. Avoid using gradients or be more subtle with them.
Lastly, I would like to touch on the point of controversial subject matter. Animation is as much of an expression of art as any other medium (which often seems to be overlooked). I value that you decided to portray your beliefs of evolution over creationism. Actually I'm proud of you for standing up for your thoughts, however keep in mind to be discreet with your opinions judging others. I know it's popular on the internet where the majority of people bash religion and creationism but keep in mind these are all theories - both evolution and creationism and the nature of the universe is still uncertain. It kind of pains me and I find it embarrassing in some of your comments how you attack these people. I personally believe in evolution as well, but this is just a theory and a philosophy, as is religion. We are no more right than creationists are, neither theory can be completely proven - that is why it's a theory.
Anyway, I apologize for the wall of text but I haven't given a thorough review in a while. Hopefully my review can help you. Good luck with the rest of your series :)