Ah yes, I managed to completely forget two points in the debate yesterday.
Firstly, as I had said, if you use points buy then your characters stats *are* choices. Even if you didn't, though, you get an extra ability point at every 4 levels - and where you put that point is your choice, therefore again making stats something of a choice.
Also, as Wormwood said, there is basically no support for an argument saying that ability scores as prereqs are a bad mechanic when many, many prc's already use them as prereqs, albeit in a veiled way. A PrC that requries power attack means that it has a prerequisite of 13 strength. The same with several other feat prereq's, like expertise or dodge - they are limiting the PrC to only individuals with high enough ability scores in the relevant areas.
The same with minimum spellcasting levels. A PrC that requires a minimum of an ability to cast 3rd level divine spells is demanding characters with a minimum Wisdom of 13, since you can't ast 3rd level divine spells if you have a Wisdom of any lower.
As such, on the basis of the myriad of PrC's already provided for us, saying that ability scores should not be used as PrC prereq's because they are no character choices is not necessarily a very valid argument.