The big difference between Guitar Hero and Rock Band is that most of the developers at Harmonix are actually musicians themselves, in bands like Freezepop, The Mighty Mighty Bosstones, Bang Camaro, The Amazing Crowns and The Konks. They know music, so their note charts actually make sense.
Neversoft, on the other hand, went from making skateboarding games to making music games. It's very rote, by-the-numbers, production line stuff. That said, Guitar Hero 5 is by far the best Neversoft-developed GH game (not that the bar was set terribly high to begin with), with a great song list and an engine that almost completely fixes everything from the abomination that was World Tour.
There are still some "what the fuck" moments, though, like charting the harmonica in "All Along the Watchtower" and the trumpets in "Ring of Fire" to the guitar.