While we don't know how a system of this type would be set up, I think there are some fairly basic issues with it that need to be overcome.
First of all, even though the number of fastpasses a non-deluxe resort guest could obtain wouldn't have changed, there would be an overall decrease in the number of fastpasses available to them. Fastpasses are a finite resource. If deluxe-guests could get multiple/unlimited fastpasses, they'd exhaust the supply faster than they do in the current situation. This would therefore decrease the number available to non-deluxe resort guests. Unless I'm missing something, the only way to remedy this would be to increase the overall number of fastpasses available, thus creating huge standby lines.
Next, I can anticipate a guest-relations nightmare when dealing with returning guests. If a guest who had used fastpass under the current system were to visit the parks under this theoretical system, he or she might be annoyed that what was previously a completely free system is now a system affected how much a guest has payed. "If it was free before, why should I have to pay for it now?" True, the arguments of "you get what you pay for" and "Well, the number of fastpasses you can obtain hasn't changed" could be used, but try using this sort of logic on an angry guest. It isn't pretty.
Finally, (and this one might not make a whole lot of sense...but here goes) there's the issue of classism among resort guests. When a guest pays to stay in a Disney resort, they are really paying for two seperate sets of benefits: the benefits of being a Disney resort guest, and the benefits of being a guest at a particular Disney resort. The Disney resort guest benefits generally apply only to things outside of the bounds of their particular resort (EMH, transportation system, etc.). These benefits are the same regardless of which resort the guest is staying at. Then, there are the resort-specific benefits (better pools, more restaraunts, etc.) that generally apply only to things inside that specific resort. These resort-specific benefits do not positively or negatively affect the experience of guests staying at other resorts. A tiered fastpass system would be a resort-specific benefit that would theoretically have a negative effect on the experience of guests at other resorts. This would be yet another guest relations nightmare. (Hope that was relatively clear...)
Sorry if I've been a little long winded on this, and I do believe that those defending the possibility of this type of system have made some good points ("Disney can do what they want," for example), however, I really do think that this would create more problems than benefits.