Philbin does two things as a head coach that I like:
1. He is excellent on replay challenges. He really is.
2. He is very receptive to change in a lot of areas where football coaches are usually extremely conservative. I've heard radio guys making fun of him for the 5 minute water break, for instance. What's funny about it? He is trying something that he has reason to believe can reduce training camp injuries. Last season he tried giving players Thursdays off. This season he thinks giving players Mondays off will be better, so he's doing it. I think 30 other coaches in the NFL give the players Tuesdays off, and I bet for 28 of 'em the reasoning is "Well, that's just the way we've always done it."
He split the practice fields in training camp to get more reps, but then went away from it for a time when he thought it was causing a problem elsewhere. He's also clearly changed his management style and the way he interacts with the players at least two seasons in a row. I actually think that Philbin's willingness to try new things or defy conventional football wisdom is a huge asset for the team.
Of course, the flip side is that I think he often 'plays favorites' with respect to who is going to get playing time, and I think he shot himself in the foot by sticking with Mike Sherman even when it was obvious Sherman was not doing a good job. I also don't see him bringing any special skills or tremendous competence on either side of the ball to the table.
Joe Philbin strikes me as a guy who can be a pretty good head coach if he has good assistants who can see to the details. I don't think he is a great head coach, but Harbaugh did turn us down.