I'll concede to this point.I thought that as long as they were socially incompetent and feeling left out it would suffice. If these are the only conditions, being special should not disqualify them. In fact, it is more likely for special people to be unable to blend in. If he said that they had to be normal, then you would be right.
Keep in mind that there is an implied negative tone to the request (primarily because it is MFauli and secondly because of the request to avoid humorous series). A male lead was specified, requiring more thought to the request than it appears. The ideal would be a variety of shoujo series (X TV, Ayashi no Ceres, Fushigi Yugi, etc).
But Pumpkin Scissors and Aquarion still don't fit. Orlando isn't the main character of Pumpkin Scissors, Alice is. She is the one dragged into things over her head (or walking right into them). Aquarion has the same problem. Apollo doesn't have any character development, the rest of the cast does, mostly Silvia. Also, when you get down to it, Aquarion just isn't that good of a series, it's just generic.
Beck is upbeat (before you argue, the anime is).
Jinto does nothing in the first series. He is dragged along like a sad puppy. He is very much scenery. He contributes nothing, his opinion means little, and the interaction of trying to understand each other doesn't mean "bigger happenings" as far as he is concerned. He is tangentially involved at best. Lafiel is the star of that series, violating the male lead specification of the request. So Crest of the Stars still doesn't work. Banner...maybe.
Pandadice is right, RahXephon fits. If I included Evangelion I should have included RahXephon as well. I should be ashamed I forgot it.