Shooting percentage absolutely is important. It's about simple efficiency. If you're shooting the ball, you shoot to score; otherwise, pass the ball and make your teamate better.
And I don't really buy that "but he shoots when the shot-clock is way down" theory, because that player is going to be taking the toughest shots anyway because they're the best players. If you compare the shooting percentage of a Steve Kerr and a Kobe Bryant, yeah, it's going to be skewed a little bit, but who cares? Nobody ever compares Kobe and Kerr. What does matter is when you compare Michael Jordan to Kobe Bryant, there is a major difference. While historically they have taken similar shots with similar difficulty, MJ in his prime shot over 50% from the field year in and year out. Kobe shot 41% last year, and his fg% has been going down each year since his career-best 46.9% in 2001-2002. Disregarding the Assist, Rebound, Steals, and Blocks categories (all in MJ's favor), his shooting percentage clearly seperates the two players.
Of course, Michael, MJ, Jordan, Mike, whatever you want to call him, is arguably the G.O.A.T. (Greatest of all time), so it's hard to use him in a comparison. But you certainly can use shooting percentage when you compare similar players. For instance, Kobe Bryant and Tracy McGrady are both right around 44.5% for their career - not a bad percentage for a guard, also not great. I'd much rather have had a young Penny Hardaway in his hay, because he shot 52% from the field. When he was shooting the ball, it was probably going to go in, and when he wasn't shooting the ball, he was probably making somebody better. With TMAC and Kobe, the same cannot be said.
Obviously, things are more complicated than simple shooting percentage. However, it's very important, and anybody who disagrees doesn't really know basketball. It's a simple matter of efficiency.