Good thread, thank you.
Yes, S.P.E.C.I.A.L. is a sacred cow. It shouldn't be abandoned, because the primary statistics give a good representation of inherent attributes of any person (plus, the acronym is just good).
Bethesda would do well to not simply cut things that are useless, as long as they have inherent worth. Charisma was garbage in Fallout 3 (also in New Vegas to an extent, but at least it did something). Is that a reason to get rid of it? No. It's a reason to give worth to it. There's no substitute to Charisma as a primary stat, it has inherent worth.
However, my idea of SPECIAL would be somewhat different to it's present state nontheless. I think the 1-10 points in each prevent each point from having an impact aside from linearly raising or reducing the secondary statistics (which can't do the inherent worth of the primary stats justice imo).
Thus we should imo go with a 1-5 point system, where each point also yields other merits. For example, a character with PER 2 wouldn't be able to distinguish friend from foe with the markers (remember, whenever there's an NPC nearby in F3/NV, you can sense it's presence - which is represented by either normal [friend] or red [enemy] markers on our compass). All markers would have the initial color. A character with 3 PER would be able to distinguish friendly and hostile NPCs. However, since you can't cram this into a linear progression system, 4 PER wouldn't enable you to even more distinguish them (as that don't make any sense).
This is just one thing the point would do. And I've got nothing against linear progressions. But a 1-10 system with features beyond those is simply not capable of containing similar worth for each point you invest.
You'd start at 3333333 and could reduce any stat to 1 or raise it to 5. You'd have 2 extra points to spend. This still allows for a great amount of possible builds (74819 I think), they'd just have more personality and character than before - and really change something in the way you play.
Such a system would bring about great changes in the overall design of course. Raising any of those would be nigh impossible (no more primary attribute raise through chems/food/equipment/etc). An Intense Training perk would be a very serious choice (in my skill system it would cost many skill points, 50 perhaps) and possible only once at that. Implants would either be cut or come at a permanent cost (such as the Fallout 2 ones - which didn't even raise SPECIAL). This would of course simplify the system to a great deal and reduce the amount of metagaming options. But that's not necessarily bad. Consequences is what we should strive for, meaningful options, not complexity for it's own sake.