People who think Federer puts more effort into slams than masters tournaments are wrong. If Federer plays a masters, he plays all out. He hates to lose.
Now, he does prioritize slams over masters, in that he'll pull out of a masters tournament if he's hurt to make sure he's healthy for the next slam/in the long run. But he isn't "underachieving" in masters because of effort.
It's because:
1. He's missed several that he would have stood excellent chances of winning
2. 3 of the 9 are on clay, where Nadal dominates.
He's won Cincinnati 5 times and Indian Wells 4, so he hasn't come up short there. You could compare Cincinnati to the US Open and Indian Wells to the Australian Open. He's won Miami and Canada (Toronto in this case) twice - he's skipped Canada 3 times since 2004, and he struggles some with the Miami surface. Djokovic and Murray blocked him from 2 more Canada titles, and that may have been partly due to them having only been best of 3.
That leaves Madrid/Shanghai and Paris. Federer skipped Paris 3 years in a row when he was dominating tennis (04-06), and skipped Madrid indoors in 04 and 05. He has since skipped both of them additional times.
I think Federer stands an excellent chance of winning Cincinnati this year again, provided he stays healthy. He may bag Paris as well, I think.