Big problem for Federer is that he needs to win a slam, and that ain't happening.
He can win all the Basels and Rotterdams he wants, if Nadal and Djokovic are going to split those 8000/4800 points between them, there's not much he can do.
This is true to an extent... in the scenario above he could make 2 finals.. or 1 quarter and 1 win (wimbledon) which is not totally out of the question.
Even if he fails to achieve this, he could compensate by performing better in ATP events than I have predicted, which, again, is not totally out of the question. For instance, if the distribution were to change (marginally) as follows:
ATP World Tour Masters 1000 (6)
Cincinatti - W: 1000
Indian Wells/Miami/Madrid - (F/2SF): 1320
Rome/Toronto - (SF/QF): 540
US/AO - SF [achieved]: 720
RG/WI - (F/SF): 1920
As irrelevant or MMish you deem Basels and Rotterdams to be in the overall scheme of things, Federer has won enough over the last 6 months or so to give himself a hefty cushion of points.
Edit: and as sexybeast points out^, Nadal and Djokovic are not totally invulnerable at slams.