Users hate change, so it’s usually best to stay with a familiar design and evolve it gradually. In the long run, however, incrementalism eventually destroys cohesiveness, calling for a new UI architecture.
This is a concept that I fought with a lot when designing the interface for the latest version of Storm Spotter. Last summer I designed and implemented a completely custom looking UI that I really liked, but I ended up scrapping it because it was too much of a break from the current interface.
I am very proud of what I ended up with though. I have a design that is a natural progression from the 2.x versions that functions much better and satisfies my need to ship something that looks a little different that it did before.