While the Johan Santana trade was in the works, there was some suggestion that his value could have been lower than expected due to concerns about an injury that he was playing through towards the end of last year. Buster Olney recently wrote:
Spoke with a talent evaluator recently who thinks that if the Twins are intent on swapping Johan Santana for a relatively modest package of prospects before the start of spring training, this may reflect some concern over the pitcher’s physical condition. In the aftermath of Santana’s 17-strikeout game against the Rangers on Aug. 19, there was some evidence of diminished velocity in the left-hander, and it was noted by at least one scout that he used his slider much less often.
There's no question that Santana was not himself after the game against the Rangers: his ERA for the rest of the season 5.11 and his WHIP 1.32. However, pitch f/x paints a different picture of what was different about his repertoire. Unfortunately, Santana's last two starts in August were not recorded. But here is his pitch distribution for September as compared to when he was cruising through May (ERA: 3.44, WHIP: 0.92):

Pitch July % Sept %
Fastball 54.3 66
Changeup 31.4 24
Slider 14.3 10.7

Although he threw fewer sliders, he threw even fewer changeups. That's not good for a pitcher whose changeup is considered one of the best in the league. Now here's the average velocity on each pitch for these months:

Pitch July MPH Sept MPH
Fastball 91.3 91.5
Changeup 81.1 81.9
Slider 84.1 84.0

According to pitch f/x, he was actually throwing very slightly harder in September. So other than a steady stream of fastballs, what was his problem?

Let's take a look at the movement on Santana's pitches, again split between July and September. The viewpoint is from behind the plate and the scale is relative to what how a pitch without spin would move (so fastballs move "up" due to backspin keeping them from dropping).





You can see that in September his Sliders are moving about 2 inches less, away from left-handed hitters. His changeups are clustered about 2 inches higher, so they were not dropping as much. His fastball was spread out more (some of them tailing almost like a 2-seamer), and he's throwing something that is somewhere between a slider and the rest of his pitches (either a hanging slider or a errant changeup). In general, all of his pitches have less of the movement intended and the groups are less crisply defined.

I'm not a doctor- it is entirely possible that Johan Santana was suffering from an injury that caused a problem with his mechanics and lead to these results. But it seems that his drop-off in Santana's performance was more complicated than him simply not throwing as hard and avoiding his slider. He was having problems with both of his offspeed pitches, and relied heavily on his fastball, instead. And even the best pitcher in the league turns into just another scrub when he only has one pitch working well.