Fafner was a giant robot show, and just like many shows in that genre it had giant robots (called Fafners) with teenage pilots fighting alien invaders (called Festum) with mysterious origins.
The problem that I had with the show was that a lot of the time I just wasn't sure what was going on. I couldn't distinguish between the elements of the plot that were being kept intentionally ambiguous/mysterious and the elements that I didn't understand simply because I was being dense.
The thing that made it more frustrating was that I was paying so much attention to trying to figure out what was supposed to be going on that it took my attention off of the real focus of the show: the drama. It's like I knew that characters were getting all emotional, but I didn't understand why they were getting emotional. In other words, I couldn't empathize because I didn't understand the source of their suffering (or whatever).
Maybe if I would have just kind of laid back and not worried about things like where the Fafners came from or what Soshi's roll in piloting the Fafners was or what this "Mir" thing was supposed to be or what exactly a "core" was supposed to be or what the message that the Festum kept repeating was supposed to mean, and instead of thinking about all of that just concentrated on the character interaction and general melodrama then maybe I would have enjoyed it a little better. But who knows? Eh. :shrug:
Regardless, by the end of the show, many of those confusing plot points were cleared up so I was finally able to enjoy it a little more. I do think the ending was a good dramatic climax, but still wasn't totally satisfying since there were still a lot of pieces that I didn't understand. I know that there is a prequel OVA out in Japan, so maybe that would help explain some plot points, but I'll just have to wait and see if that's ever released in the US.
The animation in the show was okay, but I can't really can't say that I was impressed with the job that Xebec did on either the character, mech, or alien designs nor the general action scenes. There just wasn't much of anything that stuck out. Again, perhaps the animation in the OVA will be an improvement especially since I just noticed that Production IG is involved with the production. (Maybe I won't wait until it's licensed... ...)
The only thing that I can say that I really did enjoy unconditionally was the music, which seemed almost too good for the show. Sometimes it even seemed like it was even was carrying the drama. Then there were the great music for the opening and ending credits which was performed by Angela, who is one of my favorite J-pop groups at the moment.
So in summary, I'd say if you are expecting mystery or action on the level of Evangelion or RahXephon, you will be disappointed to the point of confusion. But if you are looking for plenty of melodrama and are able to ignore the ambiguous plot elements, then go ahead and give it a try.