From my take, Hoenn has my most favorite designs as well as the worst. But mainly, the Pokemon in this generation seemed more... viscous and more menacing than the last two. They introduced that tough Aggron, intimidating Salamence (no pun intended), and the beast of the skies Rayquaza. Sure the previous two had some some monstrous designs, but they remained ingrained as childish to me. Personally, a very few Pokemon in Hoenn would be called cute. But a majority of them are definitely take a more "scary" aspect. Also, I think they brought in more ugly vs beauty Pokemon. For example, Swampert's certainly not well-defined beauty, but Milotic and Gardevoir would be agreed to be opposites of the poor mudfish.
So, all in all, take a pick. I can see that many people were actually turned off of Pokemon because of R/S, but nothing's exactly perfect. It's like every generation adding a bit more, with Gen I being the simple base. Look further at the Pokemon designs in each generation, and you can see more detail put in place, bit by bit.