1. It's not the number, it's the timing.
The Supreme Court did not hold that President Obama made *too many* recess appointments. It held that President Obama made the NLRB appointments during a three-day break between "pro forma" sessions of the Senate, which was too short of a window. The Senate said it was in session and President Obama tried to tell them that they were not.
A president unilaterally declaring that the Senate is not in session and making appointments during a three-day break is simply not a common practice. According to a Congressional Research Service report, the shortest intrasession "recess" in which an appointment was made between the start of President Reagan's first term (in January 1981) and December of 2011 was 10 days.
2. The NLRA created really easy judicial review
Some critics point to other controversial recess appointments, like U.S. Ambassador John Bolton. However, it's hard (for me at least) to think of a situation in which someone would have standing and a financial incentive to get judicial review of an ambassador's appointment. You can't just file a lawsuit because you don't like something (even if it is unconstitutional) - you have to suffer actual harm
In this case, the NLRB serves a judicial function. Under the NLRA, the parties can seek judicial review of an NLRB decision in the U.S. Circuit Courts of Appeals. That made challenging the validity of the appointments *really* easy. In this situation, every party who received a decision it didn't like from the NLRB could just file an appeal and raise both their arguments on the merits of the case and the recess appointments issue.
That's pretty much what happened. Inevitably, some circuits parted ways on their interpretations of the Recess Appointments Clause - setting up a perfect case for Supreme Court review.
3. Not partisan hackery
Some people immediately knee-jerked into cries of racism and partisan politics. The holding was unanimous, so I find it unlikely that all nine justices (including Justice Thomas) are racist and trying to block appointments based on President Obama's race. It's also highly unlikely that partisan politics motivated all nine justices to vote the same way. Finally, the controlling opinion was written by Justice Breyer, who was appointed by a democrat, as were three of the four justices who joined his opinion - two of them were appointed by President Obama himself.