I had a great time on my playthrough, so rather than try to tell you changes you should make, I'll just tell you what decisions I made and you can decide whether those are how you want people to play!
I only ever used auto-attacks, and Siegfried was my companion the whole time. (I actually went Castle-Oasis-Keep-Forest, so I didn't even meet Merlin until the very end) With how high the encounter rate is, I figured that if I went for a more spell-oriented build, I would constantly be going into my menu to drink MP potions, like I had to do with health potions. When I would get to a boss I would use Double Strike with Hero and Rally with Siegfried, and near the end I got an accessory (World Shaker?) that let me use a Bouldercrash skill that was helpful when bosses summoned help.
So I would always pick the physical choice when given one in the skill tree, though I did pick Heal instead of Taunt because I figured I wouldn't use either of them. The same goes for items; I only ever considered the Atk and ability of my equipment. Weapons that hit multiple times were always better than anything else. Accessories-wise, I always had a Pirate Map on and usually had an Unseeing Eye charm so healing would be easier as I could just heal Siegfried, but once I found the regen accessory from the Forest, I felt like I found the build that broke the game. I even switched to the armor that increased the likelihood that enemies would attack you, but never had to heal the Hero again. Which I always enjoy at the end of RPGs!
Spoilers below if you haven't finished the game!
Outside of combat and equipment, there were a few puzzles I was never able to figure out. I never found the witch's cauldron, and despite looking for an hour, never found the magic branch in the tree that the fairies alluded to in the forest. I figured out how to use the Royal Jelly, but not what it meant, and after giving the second tome to Merlin, I knew I was unlocking some kind of true-ending scenario that had to deal with what might have been getting the third blessing from the Oasis, but I couldn't put the pieces together. There was a suspicious crack in the wall in the crypt of kings and mentions of a "rift" when you go back into the first cave that I thought might be related, but that felt like a stretch.
Clearly, something's up with using Scrolls of Power vs. power you gain from enemies, but if I ever saw the downside to it, it didn't register as "Oh, this is because I used too many scrolls." It also seems to be strongly hinted that opening the door to the palace would have a negative impact on you, but I couldn't figure out what that meant, either. Since when you beat the game it asks you if you want to start from the beginning, maybe if you use few enough scrolls and exit the tower few enough times, you'll have a better ending?
Anyway, I had fun! If you'd like to ask me questions about my playthrough, let me know!