I don't think they're underrated. In my opinion, 3rd gen had the least interesting set of new pokémon and the games took away some nice things from G/S/C. Like day/night, days of the week and people calling to give you things. Plus, Hoenn was where the legendaries started to get ugly and scary rather than beautiful and mysterious.
So I think they did a sidestep with the third generation's mechanics and pokémon. Looking back, it seems like a stall before the flashy 4th gen.
BUT. I loved the music from the Hoenn games. Often better than I liked the 4th gen music. And the land itself, the Hoenn region, it was pretty nicely designed. With a desert, rain, underwater tunnels... quite a step up from 2nd gen.
All in all, I still won't be joining the crowd who screams for Hoenn remakes now. But I do think they will come.