I too prefer when the enemies are visible. In some RPGs, they can still be tough to avoid, like in Chrono Trigger and Lunar, but at least you know when a battle is coming and you can explore freely after you clear a room.

I also agree with timing attacks/defensive maneuvers. Yeah, it was a lot of fun in Super Mario RPG. I love the timing aspect of Valkyrie Profile battles, and battles in Star Ocean: Blue Sphere are practically centered around having good timing. Heck, Star Ocean: Blue Sphere in general is nothing but innovative concepts, like the complex way in which moves are learned and skills are built, item creation based around mini-games, and so on.

I love real-time battle systems. ATB was a good start, and Tales and Star Ocean took it to the next level.

I like when you have the option to have spells target different amounts of enemies, with damage inflicted divided accordingly.

I also like the "limit break" style system of Lufia 2. It was a lot more interesting than in Final Fantasy VII, since it was based on the properties of your equipment, with loads of different things you can do, each using up a different portion of your bar. It added a new factor to equipping, since you might want to keep a weaker weapon or piece of armor just because it has an awesome ability.