All three mental stats could use some boosting, IMO, although in a skill-oriented game they're all more valuable. Incidentally, IMC this hasn't been as much of a problem because of one of our other house rules:
There are classes that can raise DEX at all costs (Rogue, for instance), resulting in a ridiculously high Reflex save. There are classes that can raise WIS at all costs (Cleric, Druid), resulting in a ridiculously high Will save. For everyone else, there's a problem; if you're a CHA-centric class (Sorcerer), none of your saves would be pumped up by your high CHA.
So, we changed each save to use two stats.
Fortitude is as much a question of physical fitness as the ability to absorb damage; there are plenty of people who are in excellent shape but who can't take punches all day long.
So, instead of adding CON bonus, you add (STR bonus + CON bonus)/2, rounded up.
Reflex isn't just about dodging quickly; you need to know where to dodge TO. An intelligent man who figures out where the Fireball is headed and knows exactly where to go to avoid it is just as capable as someone who can move quickly but doesn't know which way to go.
Instead of adding DEX bonus, you add (DEX bonus + INT bonus)/2, rounded up.
Will is as much about force of personality as the ability to see the world around you for what it is.
Instead of adding WIS bonus, you add (WIS bonus + CHA bonus)/2, rounded up.
What does this do? Well, for one thing, it makes +save items/bonuses more valuable. Under the core rules, I don't know anyone who'd use an amulet that added directly to Will when they could just get a +WIS item instead. Now, instead of a +4 WIS item raising Will by 2, it only would raise by 1. (The other effects of WIS would still often be worth it: skill bonuses, spells for divine casters, AC for Monks, other class abilities.)
Also, it makes STR, INT, and CHA more valuable, even for the classes that didn't need them. I know, STR doesn't really need to be more valuable, but when half the group has STRs of 10 or less because they're spellcasters, and the archer only has a 12 because she had really good rolls, it IS a dump stat. Finally, it makes a substantial difference between Wizards and Sorcerers; Sorcerers would have a high Will save, while Wizards would have a good Will save (from the class) and a good Reflex save (from the INT).