Man...where can you start with this show. I guess the 1st thing I can say about this show is definitely not for everyone to go watch it as it doesn't follow the similar path of a sci-fi anime at that time. In most anime we watch, they have some sort of genre it try to follow and most audience will set the right mindset or mood when going into the show.
For RahXephon, the mood is very different and it's better to keep your expectations to low or none when going into this show. This isn't a mecha anime as it's the least important aspect in the show even though they is some mecha battle sprinkle hear and there to get the audience interested. Majority of the story when I watching is very heavily character driven to the point the pacing of the show is very slow and sometime come to crawl. Yes, they is some battle scene in the entire show but you either see them mostly in the beginning or as you get closer to the end.
For most audience, RahXephon have quite a similar feel of Evangelion which is true. The parallels between this two show have some similar idea. Both have a young male lead who was force in a situation where they need to pilot a mech for an organization to fight against an enemies they don't know much. They both have an older female character who protects and shelters the main character during the show. Both take place in a time where Tokyo manage to come out of some sort of post destruction and they become the last line of deference to protect against the alien threat which try to destroy Tokyo. Even with this similarity, RahXephon isn't like Evangelion. It doesn't dealt into psychological tone with a mix of Christian undertones which Evangelion do. It more dealt more into the drama with the people around the main character and the romances between them.
As for the story, I won't synopsis the entire story as you can find this on wiki but I will say the story isn't too simple to follow and linear but at the same time, it isn't too complicated. As you watch the show, they're quite a few elements of mystery which get very confusing or you might get lost if you don't pay attention. This mystery will eventually explained or resolved if you keep following what happen during the show. The story didn't give much away from the start and how they information is revealed is good.
The animation look too simple and plain when you start watching. It feel flat and the color is solid type which you don't see too often in most anime. This grow on me quite well that it didn't brother me as I continue watching the show. In a way, you can say it might be the strength of the show as this simple look does make the show look unique by itself.
The biggest strength I say for the show is the character development. Majority of the character in this show is developed well in the story (except for the few who could've been develop a bit more) and feel believable for the most part. The only issue I have with some of the character is I wish their elaborated more on the character motives on some of them as it was difficult to understand the reason for some.
Overall, I kinda like the show but did get confuse during the process of watching it. I guess not in the right mind make it harder to watch for a bit and also my work kinda postpones watching the show for a while. Still, I finish the show and would recommend to people to have a very open mind going in and like story and character development more than the action scene as this show is literally that.