If they're there and I can't battle them, there's no point them being there in the first place. It may add a bit of life to maps, but if they're also going to behave differently to how I think they should (i.e. I should be able to battle all wild Pokémon, which isn't unreasonable), then maybe you should just make better maps instead.
Another reason why I wouldn't be fond of them is that the Pokémon lurking in tall grass are completely invisible. Of course they are; there's an infinite number of them, and it's hard to fit an infinite number of sprites in a finite patch of grass (no, really). If I can't see the important ones (the ones I can battle), why can I see the ones that are decoration? And if I can battle the decorations, why are they still different to invisible grass-based mons?
I think if you're going to show Pokémon bobbing around in the overworld like that, you need to go all the way and have them be the only way you encounter Pokémon. And the only way I can think of is to load a finite number of bobbing Pokémon when you enter a map, be able to battle just them (no spontaneous encounters), and then reload some more when you leave and return (or after a while depending on the current population). I seem to recall the Mystery Dungeon games doing this.
Of course, that's too difficult to expect just anyone to program (although it's probably easier than you think). The trick would be to make them stay in their regions (in the grass/water, although cave dwellers could just wander anywhere). It'd be different, though.
On the other hand, the various legendary Pokémon, Snorlax, Sudowoodo, Kecleon, Drifloon and so forth all stand around waiting for battles, and they're fine for no reason other than we're used to it because all games do it. But these Pokémon are important, either by being roadblocks or specials/legendaries, and having them be visible makes that clear and is the distinction. If you can see it, it's special.
So on the whole, I think that while they add a little to the atmosphere, it detracts more from the gameplay by being inconsistent with the rest of it.