i loved isometric in some games. baldur's gate was awesome. recently however i was playing planescape torment, and seeing as the environment was quite alien, i couldnt tell what was door and what was crate. i think isometric works well when dealing with environment that is familiar, it can make game more beautiful than full 3d because you see it as a whole, and not just what is in your field of view. sometimes environment is fantastic, but you just look in the wrong way and miss it all.
so, it is great when it fits correctly, and bad when not. yeah, i know, its mindblowing.
as to missing it? i preferred isometric when 3d was new, because you could get incredible realistic 2d, or crappy blocky 3d. but nowadays, i think it could work in indie games, because i dont think you can justify 50/60$ tag on 2d game.