I much prefer Citymapper. It's less buggy (I lose the current directions at least once per direction with Transit...) and much faster (searches, times). It also displays where you should be in the train so you can get out faster. But in the city I currently live, only Transit exists
I tried both for a while. I liked The Citymaper UI better, but Transit actually shows the live position of the bus. Transit wins. This is with VTA in Santa Clara, California.