The radical difference would probably be the extreme usefulness of the Ninja and Sage over the other classes in the Famicom version, so much that your party could consist of Ninja and Sages and you could beat the game with ease.

You will gain many levels going through the final dungeons, so do not worry about having to level up. Going through Eureka, and Sylx Tower, and the World of Darkness should have you in your mid-50s before the final boss. But a little leveling wouldn't hurt, especially if you're going to buy Shuriken. Proper damage output and healing are the key factors to beating the final boss.

I would also recommend getting Leviathan and Bahamut, since they are pretty powerful summons and can help against the large groups of enemies you'll encounter.