I'm torn about them. On the one hand they free up the combat design to be as wildly different from the exploration as it wants. Which can result in really creative stuff. Favorite examples are Undertale, MegaMan Battle Network series, and Tales series.
But on the other they interrupt the flow of exploration, the music, you forget where you were by the end of combat and they can be very annoying if they happen to be common or just as you're about to leave an area. The consolation prize of growing stronger with every battle only helps so much.
I don't hate them, and actually think they improve dungeon crawlers like Etrian Odyssey.
But for other games I think they slow down the pacing too much, especially when you want to get back to an older area, as you are going to fight lower level enemies and there's usually an unavoidable scene transition which takes time.