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 really like random battles for the most part, but they are not normally the thing that makes or breaks a game for me, either.
Some of the first jrpgs that I remember handling battles better then the typical final fantasy was Chrono Trigger and Pokemon. In Chrono Trigger, you can typically see the enemies before you have to fight them, though they would often surprise you with enemies that you couldn’t see jumping out. I think that worked much better than just the normal system where if you walk around long enough you get a battle. Then Pokemon has 2 different things that it did. First, for trainer battles, you can see the trainers on screen so you can make sure you are prepared before you go into a fight. Then for the normal battles around the world, it does use random encounters, but they take place ONLY within certain spots, like in tall grass or in a cave. So you still have a lot of freedom to roam around in areas without triggering battles, and when you do go through those spots, you know that a battle could pop up, so you can be ready for it. There are also items you can use to avoid encounters.
For dealing with the annoyance of low level enemies, I think Earthbound had a pretty good system. In Earthbound, it shows you enemies on screen rather than doing random encounters, and once you get to a significantly higher level than the enemies, they will run away from you instead of coming at you, so you are free to just ignore them.
I agree these games made big improvements but I still see them as bandages to the inevitable problems that came with random encounters. There’s no undoing the interruption of flow you know.
I think it’s a tradeoff though like I said. Because I don’t know how you can have a combat system as cool and creative as say Undertale (blending turn based and realtime bullet hell) or battle network (blending turn based, real time and card game) without it being completely separate from the overworld.