Fighting the engine?

I started building a pokemon-like with MZ and got the battle system working. I was happy with it but at a certain point I was fighting (?) with the engine. For example, at one point I realized I was creating objects and battle formulas that weren’t using the engines database.

Is this a common experience?

I was of a mind that I could release some of this publicly but as an add-on I feel like people would have a hard time using it.

I ended up moving to Unity but there’s so much I have to rebuild it really killed my momentum.