I do want to offer a bit of design advice here, but I think your idea on how to develop skills could be interesting and add something to the game (assuming its not a severe hindrance to game flow).
The problem with RM2k3 is that damage from spells and skills were very hard to control due to the limits of the system you were given. Upgrades and tiered spells are by far the easiest to implement in this version of the program.
The difference between the two systems, however, is important to know and understand:
Upgrades: remove the previous version of the skill and learn the new, more powerful, version. This keeps the spell list tidy and to the minimum, but prevents players from choosing a weaker spell where the more powerful is a waste of MP in terms of the damage required to kill the target.
Tiered: all previous versions of the skill are retained, meaning all skills (including their lower strength counterparts) are available to use. Unlike the above, this leads to a larger spell list but gives the player control over which version to use.
If you intend to have a lot skills/spells, I'd suggest going with the direct upgrades method. A player does not want to wade through 50 skills to get to the one they want. If you only have a few key skills, however, a tiered system may be a good choice.
Above all, though, think about the player and what they may want and need to use and how your game works. If MP is of no real concern and you aren't needing to conserve MP all the time (it's not a rare commodity but is a common resource), then upgrades is perfectly fine. It doesn't matter if you spend 50MP to cast the 3rd upgrade of Fire, when you only needed the 2nd upgrade that cost 30MP. That 20MP difference is easily restored.
On the other hand, if your MP source is a limiting factor and you aren't going to be restoring it very easily, then tiers are better for your game play, even at the expense of a large spell list. Being able to decide whether or not to cast Fire 1, 2, or 3, is incredibly important, especially during the early to mid game where MP sources are at their scarcest. The last thing you want is your player running out of MP quickly when he is only half way through the dungeon/to the next restore point/inn.