I think there might be a severely overlooked factor in play for scarcity of issues, and it can easilly be illustrated with the FF #48/49 discrepancy case. In all likelyhood, both distribution and sales were quite similar for each issue, and I do not believe that one was found in warehouse troves whereas the other was not. The actual deciding factor (in my opinion) was the number which were saved by collectors in the 70's. I collected in the early 70's, and EVERYONE knew FF#48 was the first appearance of the Silver Surfer. Less than 10 years had passed, but it was already recognized as a collectable. No one cared that #49 was the first cover appearance, nor even cared about the #50 either. When a copy of #48 appeared it was quickly snapped up by collectors, bagged and backed, and put away.
That to me explains the discrepancy quite well. Collectors may not have hoarded them in the 60's, but by the time the 70's rolled around, they were a staple in the serious collection. #49, #50, etc were never treated in such regard, and therefore were not preserved in the sheer numbers which #48 attained. You could find worn copies of FF#50 getting dog-eared in 10-cent boxes at every convention, but #48 was aways up on the wall. This "reverse preservation" has depleted the supply of #49 and #50 over the years, leaving far fewer examples of high-quality specimens than their big brother #48.
As for pricing, it's still a [#@$%!!!]-shoot. Demand for #48 will always be higher than for #49 or #50, and likewise the later issues will always be in tighter supply. It is up to the market to decide which ones have more value on any given day.
-Rival