There are several potential problems with this entire idea:
1) If done by an Archmage (as pointed out previously), the spell leaves entire squares open. Hence, there are ways to exploit this (Flying Monk from above, Stinking Cloud spell with an origin point more than 10 feet away if the shape has squares that allow it to be cast out from, etc.).
2) If done by the Extraordinary Spell Aim feat, it can be ruled that it is even more ineffective. Just because the Antimagic field does not affect the creature (i.e. the caster) does not mean that the DM cannot rule that it still affects his spells. All of his spells. This would make a caster pretty vulnerable.
An example of this in the game is an area effect Dispel Magic. It targets the spells on the caster, not the caster himself. The inverse could be true (the antimagic does not affect the caster directly, it only affects his spells).
3) If done by the Extraordinary Spell Aim feat, the spell has a DC 31 Spellcraft check. Not hard at higher level, but usually not automatic either.
4) Antimagic Shell is one of those unusual area effect spells that emanates from the caster. If you make him immune to the spell by "shaping it around him" (via ESA), it could be ruled that the spell fails. If it is not in his area, then it is not in the area of the point of origin, hence, it cannot emanate from that point of origin.
"A burst, cone, cylinder, or emanation spell affects only an area, creatures, or objects to which it has line of effect from its origin"
The line of effect could be ruled to be stopped by the "immunity hole". In other words, the caster is "totally immune" to the Antimagic Field spell INCLUDING the emanation of that Antimagic from himself.
5) Antimagic Field moves with the caster. But if the caster is unaffected by Antimagic (via ESA), he cannot be affected by it in any way. Including it moving with him. If it moves with him, it is "protecting him" and hence affecting him (in a positive way). But if he is unaffected by it, how can it protect him? Hence, if he is unaffected by it and moves, it stays put.
This could be ruled as a situation of "you cannot have your cake and eat it too", especially in the ESA case where the caster is unaffected by the spell.
And finally, one way to defeat this tactic is to have your own Wizard cast Fly, get slightly above the Shaped Antimagic Field Wizard, and then cast his own Antimagic Field. He will drop into the area of the SAF Wizard and then both of them will fall to the ground (doing this at a high elevation is risky). The rest of the group then mobs the SAF Wizard when all of his magic is gone (remember "two antimagic fields in the same area do not cancel each other out, nor do they stack", since the SAF does not cancel out the normal AF and vice versa, it does not prevent it from working).
