D20 Modern suffered from being too generic. While the rules were sound and fun (I still play it) it has no real "core flavor" to it and thus it can be very difficult to determine just what and how to run it for a GM.
I wholeheartedly agree.
Truth be told, I prefer the D20 modern system to 3E. I just found the generic classes, feats, talents and overall flexibility to be great. But as you said it never really had an identity (core flavor) and IMO it suffered because of it.