Criticism of the back-and-forth between the two versions is valid in that nobody had agreed on the cost of switching the ships to CATOBAR or when it would be paid for.
On the other hand, if we're talking about dependence versus independence on non-UK equipment, it is not good to be totally dependent on a single sub-type of a foreign product, that has only one customer other than the UK.
And as we have since discovered, timing is a bit of a non-factor since combat-ready JSFs don't appear to be in the cards before 2020.