Grog said:
"Not everyone's going to take it" isn't a defense. You can say that about ANY feat. It has no bearing on whether or not the feat itself is balanced.
To add to this, an unbalanced feat is an unbalanced feat regardless.
In the case of Indomitable Will, the DM always used to have his Enchantment (and even certain types of Illusionist) specialist NPCs throw Charm and Hold and Dominate, etc. against the PC tanks because it was obvious to the NPCs that these PCs should be the most susceptible to those types of magical attacks.
Now, a PC Fighter or Barbarian takes Indomitable Will. Sure, it cost him 3 feats. But, the DM is now stuck in a situation where only Reoccuring Villain Enchantment Specialist NPCs should eventually figure out that you cannot charm the PC Fighter. Every other Enchantment Specialist NPC should by default target this Fighter (at some point in the combat) and waste a few rounds every combat finding out that the Fighter almost always saves. Not only that, but it changes other aspects of these types of encounters. For example, if the Fighter saves more often because of this, then the Cleric and/or Wizard does not have to cast as many Dispel Magic spells to counter a Domination.
Eventually, it becomes so bad (and boring) that the DM stops sending these types of NPCs against the group.
And, it is all due to the fact that the feat is unbalanced. Remember, this feat can be acquired at 3rd level. +2 to Will saves is balanced. Two Will saves pick the better of the two (both at +2 btw) is not. Any game mechanic where you can roll two D20, pick the better of the two rolls and oh by the way, you can do this every single time this roll comes up in the game and are not limited to set number of times per day (like one), the feat is unbalanced.
Third level Fighter with Wisdom 10 has +1 to Will saves. Against a third level Cleric with a 16 Wisdom and Hold Person, he saves 35% of the time. If he takes Indomitable Will, he saves 69.75% of the time. Effectively, he just got a +7 to his save, +5 more than taking Iron Will alone, the equivalent of a +5 magic item for a feat.
No feat in the game so far gives +5 to a save TMK. This one easily can.