Yeah, that's basically problem with RPG Maker combat, even if I tried to make things better. I'm currently experimenting with various plugins and systems to overhaul combat - final chapter for sure will feature completely different combat system.
In large part, yeah. Working with RPG Maker is a ton of fun, but it's hard to take the tried and true turn based combat systems and have it feel unique and immersive. I like a lot of what you did with the combat in this chapter. I can't give an in-depth explanation into why, since it's been quite a while since I've played the game and don't want to replay it at the moment, so a lot of the nuance escape me. But I can tell you that I remember liking the overall feel of the combat.
There were two things in particular which I remember bothering me with the combat.
First was that enemy initiative was just too high. Pretty much every time I entered combat, nearly all the enemies would end up going first. This persisted throughout the game regardless of how high I tried to stack initiative, and there honestly really aren't that many ways to increase it. The problem with this is that it just doesn't feel good. Going into battle and then sitting there for a few turns getting beat on before you can act is simply unfun. The first few turns set the mood of the battle, and those turns seemingly always belonged to the enemy. There were times I went into battle naked just to get the first hit, and even that only worked rarely. At the very least, I'd say that Alan should have gotten a first-turn initiative bonus so he could reliably go first in order to allow the player to use one of his tanking skills to direct the flow of combat from the very start. With how it was, by the time Alan got to act as a tank, my party was likely half-dead across the board. So even when I did finally get my first few turns in the battle, I was best off spending them spamming potions. Then, finally, as my second turn rolls around, I could actually start going on the offensive and dealing damage.
Second was that skill selection was so very scarce. I was spamming Attack just as often as not. When I was using skills or magic, it was usually a single, low-cost spammable which is, for all intents and purposes, just a stronger "Attack" option. Prime examples of this are... *opens game to look at skills* ...True Strike and Flame Bullet. Quite frankly, having a spammable skill that basically just does more damage than Attack is about as fun as just spamming Attack. You may as well have just buffed Attack at that point. All it meant was I had to not deal damage every so many turns to recover MP by using a potion. The lack of healing skills also meant I was spamming potions for direct healing instead, which isn't exactly exciting.
The first of these problems makes the battles feel unnecessarily drawn out, and the second makes the time spent in battle feel uninteresting due to lack of options to achieve victory. I feel that fixing these two things would leave you with a more immersive combat.