I think you guys might be looking into the whole thing a little too critically. Remember, the leveling, update of weapons, armor, and abilities are all tied to gameplay,
not story.
The best analogy I can think of is in the case of the Resident Evil series. In that series, your character can be bite by zombies, slashed by Hunters, and mauled by every sort of monster, all of which are infected by a deadly and communicable virus. However, no matter how much the character is hit, he/she never really suffers the effects of the virus. That's because he/she's not supposed to ever be hurt as defined by the storyline.
Point in case, Crono getting killed by Lavos, then coming back and wailing on the beast, taking hits that were actually stronger than that one attack and surviving. In the end, if it's not designated by the story, it's never happened. Every person remains at what could be considered a "normal" state, in which even Magus could be taken down by a single blow from a sword (much like Aeris was). The sole purpose of HP, MP, leveling, and all that is for gameplay, not story, because, let's face it, if just about every attack from an enemy were to work as it would in reality, then even Goblins and Imps would be deadly enemies throughout the entire game.
That would mean that, skill wise, Lucca never managed to improve any from her natural state. (How could she have beaten Lavos then? Lotsa dodging, grit, and having the script on her side
).
At least, that's the way I've always seen it.