I think the inclusion of too much 'trash' encounters is one of the things that holds back RPGs the most (not just JRPGs). I generally see three ways to mitigate this:

1) Make the game harder
Each random encounter has the potential to seriously harm you if you aren't on your A game for each. Even an encounter that you have already cleared 10 times isn't something you can just zone off for, differences in the RNG are significant enough that you have to have slight tweaks to your strategy.

2) Meaningful difference between excellent and mediocre performance in battle. Whether it is a tough dungeon where resource management is a problem, or a system which increases the rewards based on battle performance. My favorite version of this was Mega Man Battle Network I. While not a fantastic game each battle had a chance to get a reward that was increased by not taking damage and killing the enemy faster. Also HP was re-filled after every battle. Because of this each battle was you trying to go all out and nail that 'perfect' fight, rather than just playing it with a routine safe strategy.

3) Make the regular gameplay fun. The encounters between bosses shouldn't be filler, they are THE GAME. Look at FF1, though not a shining example of deep gameplay, it wasn't necessarily always the bosses that were the difficult part. I also think of FFT, where random encounters make a huge chunk of the game, not as filler, but as a part of the legitimate gameplay experience.