The rate wouldn't change, except a little for each player 3 stats/9 would give basically the same as 1 stat/3.
This is not true. If you've averaged many stats to the same relative plateau it is likely the same, but if you've min/maxed as many people do and one of the three stats listed is lower, the effects will be more than noticable. Think of these two cases: con 100, end 90, wil 90 vs con 120, end 90, wil 35. While the former results in a less-than-drastic 33/31 for old/new, the latter results in 40/27 which is very clearly a great difference (The old system would have resulted in 148% of the new system's FP regen, in this case). This is not an argument against making any change, or even this change in particular. Just a refutation of the argument that there would be no big difference.
Willpower in the fantasy setting is usually referencing the mind-over-matter view we're all agreeing on here.I don't think willpower factoring into how long you can fight before you can't anymore is a stretch.
The notion that willpower factors into maximum FP is how this ability to push beyond the limits of normal folk is represented. It is the "capacity" to keep going when other people would quit.
Thus far I don't see any real arguments in support for willpower being used to calculate fatigue regeneration. It appears to have been a suggestion more than an articulated stance. I would argue against willpower having anything to do with regeneration of any sort, excepting through the use of magic, for the reasons stated above. As a capacity (read as: max fp modifier) it reflects the will or desire to keep going. In terms of recouperation, constitution and to a lesser extent endurance fit that bill nicely. Is it meant to represent actively slowing your breathing and raising your arms above your head like they taught in phys ed? A measure of determination not to appear winded that results in actually being less winded?
In other words, I am skeptical of willpower's potential role in FP regen rate.