I can't speak to Lucia's Nether Flame Skill as I don't have that character. Maybe an earlier character I've forgotten? As for Lilith's Voodoo Cure (Juju Balance), I use it quite a bit. I tend to use it when a player's HP is nearing 50%, not wait for it to get below 50%. That's probably going against the grain of your desire (to prevent players from spamming healing skills without thinking of other strategies), but I am not a very complex game player. My warriors fight, my healers heal, and my mages spew magic. I've never had a problem with either Lilith or Leonardo running out of MP. HP and MP are regenerated a bit each turn during battle and fully restored upon level up. The drops are very generous, so between blue potions (50 MP) early on and cyan potions (300 MP) later, MP has never been a problem.
Edit- found Lucia, she was an earlier character at the Ice Temple. I remember that I had to be careful not to wait too long before healing because of the initial drop in HP, but it didn't prevent me from using that skill. I don't remember having an issue with her MP running out, though.
In general, I will admit that trying to understand what each skill/spell does can be quite daunting, but I usually just dumb it down to something like 'okay, this is a fire spell that may or may not cause a lingering burn state.' There is a bit of a learning curve to using an aid skill before the active spell/skill, but once you get the feel of it, I believe it adds to the battle experience.
That said, I am probably not the best person to critique battle play because I'm just not the best tactical battler.
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On another subject, I just restarted the game and I'd like to make a request. In that opening scene where Morrigan is rescuing Lilith, there is quite a bit of tutorial text. I don't mind that, especially since there seems to be a way to skip it if desired, however, when you do choose to read it, the last dialogue is the 'Do you want to read this again?" choice. Unfortunately, the default choice is 'yes' so if you're just quickly reading and spacing your way through the textboxes, you've all of a sudden found yourself being forced to read all that text again. Is there a way that you could reverse that so that the 'Thanks, I've read it and I'm good to go' could be the default?