They highlighted the tactical disadvantages in The Best Of Both Worlds. In a battle situation, the saucer section’s phaser banks, impulse drive, and fusion generators are of high importance.

There are also alternatives. In DS9’s episode introducing the Jem’hadar, The Odyssey simply dropped off their families before heading to the Delta quadrant.

I’m the event a hostile force is encountered, it is likely the saucer section would just be pursued and destroyed, as it could only flee on impulse or sustain a low warp is released at warp.

So they really only used it the only times it was practical: facing Q, facing the arsenal of freedom (as the automated system only attacked ships in orbit), and as a life raft after the star drive was destroyed as in Generations.

It might also be noted that prior Enterprises had the ability to separate the saucer on an emergency. It was just never used on screen, and also would probably require a spacedock to reassemble.

I personally think it was just an experiment that didn’t work out. Perhaps they just reverted to emergency separations.