There isn't a huge balance headache here. Sure, you could stack Iron Will on top of itself ten times... but that'd still leave you vulnerable to Fortitude saves, Reflex saves, and any spell with no saving throw. So it's not like you'd suddenly become invulnerable to magic.
That being said, I dislike the basic concept of the flat +2 bonus. It's just boring; sure, it allows you to shore up a weak point, but it does it in a way that's inferior to the normal leveling process. Feats like Skill Focus are the same way to me; sure, the +2 is nice sometimes, but if it just does the same thing normal skill raising does, then it's just not appealing. So, IMC, we've changed quite a few things that add flat bonuses.
Skill Focus, for instance, doesn't give a +2 bonus any more. Instead, it gives you two abilities: first, you can now Take 10 on that skill even under duress; second, you can re-roll a skill check if your original roll was a 5 or lower (which raises the average result by 1.875), and the new roll stands.
Greater Skill Focus keeps the Take 10, allows you to Take 20 on the skill even if failure would have a consequence (basically, you're working it out in your mind for a while before doing it right the first time), and you can re-roll a skill check of 10 or less, but the new roll stands.
(All of those +2/+2 feats like Alertness can stay as they are now.)
So if you wanted to do something similar for saves, you could. How about this:
Iron Will: On a Will save, you can roll an extra d20, and use the higher of the dice. However, you suffer a -2 penalty to the result. This feat may be taken multiple times; each time adds an additional die to the pool.
(with similar versions for the other two, of course)
One d20 has an average of 10.5. Best of two is average 13.8, so even with the -2 you're gaining 1.3 on average. Best of three averages 15.5, gaining another 1.7; Best of four averages 16.5, gaining another 1.0. I was tempted to have the penalty be more Manyshot-like (-1 per die used) but it doesn't scale the same way, since the Manyshot damage increases per arrow.
But the benefit's bigger than just the effects on the average. Your chances of getting really low rolls drop fast, as do your chances of getting a really high roll. If all you needed to save successfully was a 5 or higher, you previously had a 20% chance of failure; even with the -2 penalty, two dice drops that to a 9% chance, three to a 2.7% chance, and four to a 0.8% chance. On the other end, maybe you really needed a good roll; if you needed a 15 or higher to save (30% chance), even with the -2, two dice raises your odds to 36%, three dice to 49%, and four dice to 59%. Sure, flat +2 bonuses would have similar effects at the extremes, but this is more fun, and critical 1s are far less likely.