The problem is not really with the system; I've managed to make a fun and engaging game without a single script (for practice).
The problem is that the default encounters ('Troops') are BORING. To a one they're either sIngle bosses with buckets of hit points, or groups of two or three of the same enemy. Which is fine for what it is - an example of how to set up encounters - but not very fun to fight.
The solution is clever encounter design. I made a troop with three characters as a boss battle - one healer/support character that threw out status effects, one striker with high Defense and low Magic Defense, and one mage with high Magic Defense and low Defense. It was balanced for 30th level default Actors and it was a lot of fun.
The problem is treating the system as something other than what it is - a guideline and example to build on.
Edited to add: Having a lot of meaningful tactical options - read, having either high level Actors or tweaking them so that they have a decent array of skills at low levels - is mandatory here. Same principle applies, really. The default classes start to get interesting at around 5th level.