Mesh- I'm a fan of fighting games as well, so combo systems like that and Valkyrie Profile have a soft spot with me. It can add spice to the turn-based broth, if done properly. Gear battles were a pain because I was always monitoring fuel consumption. Xenosaga II's battles were a pain because it was a crapshoot finding the one best way to defeat an enemy. Last Rebellion was Xenosaga II's battles done better, but those battles often ran too long.
Of course, regular garden-variety turn based systems can either be good or bad depending on a lot of factors. A Witch's Tale, for example, made every battle an absolute chore thanks to lousy balancing and battles playing out way too slowly.
As for party-chat, the Private Actions were always my favorite part of any Star Ocean game. I'm not a Star Ocean fan by any stretch, but the Private Actions were a good idea, even if many were just plain doofy (I almost spelt that oddfy) owing to some WTF? characters (i.e. most everyone in Star Ocean 4.)
One "innovation" that seems to be a double-edged sword is save-anywhere. Saving anywhere is great for when you have to suddenly leave the game. On the other hand, you can get so engrossed that you forget to save so occasional reminders to save aren't so bad, kinda like save points. Go figure, eh?