I'd prefer to have both fleshed out. The whole genre has been done so many times, I don't think there's an excuse to have a crappy plot or a lame battle system anymore.
But I own RPGs that have awesome stories but only mediocre battle systems, and I still love them a lot. I guess the plot tilts me more than anything in a role-playing game.
Many people did not like FFX's amount of cutscenes, but if you sucked all those out of the game and only gave one at the beginning as a general set-up, you'd be left with...running down a road and sometimes clicking things from a menu. That isn't fun at all. The battle system is interesting, but can't carry all the weight of the game. Xenosaga Episode I has a very deep battle system, hugely deep, but it still has flaws (namely ridiculously long tech animations), and Episode II's is also very original. I would describe both as fun and I have fun playing it as a game...However, the great Jubbah sure knows that after so many hours I wasn't playing Xenosaga Episode I or II coz I like to stock AP.
The traditional turn-based RPG formula is only interesting to me as an entire package. Taking away an involving plot leaves only repetitive combat where you choose "this option for this monster" over and over. I would run out of motivation to bother finishing it.