I'm just the opposite of everyone I suppose. I liked Team Magma. I thought they were pretty sweet. The gym leaders were cool. Day/Night isn't really all that great if you ask me. In D/P/PT it is, but in Gold/Silver it was sort of this cheap 'cool' thing everyone raved about. I liked the addition of the Battle Frontier in Emerald especially. Also, adding EV training and natures made the games way more complicated than necessary, but at the same time it was a great addition, because it made the games so much more competitive.
As far as the Pokémon go, I loved the third generation. Blaziken, the now infamous Mudkip, Groudon, Rayquaza, Kyogre, Latios, Latias, Absol, Metagross, Salamence, Gardevoir, Mighyena... there were quite a few favorite Pokémon in the games. This was a vast improvement in my mind from G/S/C. In those games there were not many I liked. I did like the legendary dogs, Tyranitar, Scizor, Espeon, Umbreon, Skarmory, and Houndoom, but I found most of the Pokémon from the second generation to be odd looking, and not very cool. It was sort of the same with D/P/PT. There were some new ones I liked, but most are just weird.
That being said, I will of course be buying HG/SS and will probably love them. It has been forever since I have played those games.