My main pewee is with the smart defense ability of the scholar I really don't think this ability should be used with armor or similar abilities like the monk's AC bonus from wis.
Well, I will try to respond to this. The basic archetype of the scholar is "be smart, give good advice, and not die." Other than a bunch of knowledge skill bonuses, that is about all a scholar gets until second level. I didn't see any reason to exclude scholars from wearing light armor. The only reason to keep it from mixing with armor is to make the ability weaker, and I did not intend for the scholar to be weak. In 3e, the Swordsage and some versions of the Bladesinger can get Int to AC in light armor. Saying the scholar's Int bonus to AC is strong is a little like saying the fighter is strong in feats, or the barbarian does a lot of damage. Intelligence typically has little or no combat uses without class features to bring it into play. If the scholar pumps up their Int, that means points or magic that could be going into Dex, Str, Con, or even Wis, all of which have direct bonuses to combat on their own. Considering that Dex already adds to ranged attacks, AC, Reflexes and initiative, I think this ability grants, at most, parity with rogues and monks.
If it didn't stack with armor, the class would become a one-level dip for wizards, or characters would simply start wearing better armor, either by taking a level in fighter, wearing light armor, or smiply eating nonproficiency penalties, making the ability moot.
My player who is playing a scholar/fighter/martial artist has insanely high AC and most monsters need a 20 to hit him. The stacking of bonuses from agile defense, dex, dodge armor and the smart defense ability is to much IMO.
First of all, let me say that a scholar/fighter/martial artist sounds really cool. But moving along to balance issues, what AC are you getting at what level? A straight up fighter should still be able to beat him in the AC department simply by wearing heavy armor. Going from a chain shirt to plate is worth 5 AC alone, and you would need to be at least 13th level to get any benefit at all from Agile Defense in heavy armor.