What was the Japanese exclusive content in Cave Story 3D

There are 3 different endings.

Getting the worst ending involves opting to end the game early by talking to a certain NPC. You won't get to do the final dungeon sequences or fight the final boss. You can always say "No" or just not talk to the NPC, so it's not something you can really accidentally do or get shoehorned into.

The normal ending is gotten by following a standard playthrough, turning down the option to end the game early, and going through the final dungeon and boss. It's fairly straight forward, and what you'll most likely get on your first playthrough.

The best ending is achieved by following specific requirements at certain points in the game. It's very difficult to explain without any spoilers, but it involves skipping certain events and items to get better items at a later point, and making sure you follow through on an optional sequence of events. This opens up an extra dungeon after the final boss that would have to be cleared. Few people achieve this ending without knowing that it exists and the required steps, as they are fairly unintuitive at some points.
A guide to getting the best ending can be found in this question, if you wish to see how to get it.

The thing about weapons in cavestory, is that getting hit will cost you XP. Your weapons gain XP so quickly, becuase if you get hit at all, you need more XP to recharge.

This is especially true with the Blade, where even losing 1 single hitpoint is enough to knock you down from level 3 to level 2.

There's also a weapon later on in the game that is most powerful when it's level 1, and actually decreases with "level ups".

You gain XP so quickly because XP tends to fluctuate quite a bit anyways.

This doesn't change based on the difficulty level, but if you're on Hard, that means you're invariably losing less XP from getting hit, because getting hit usually means you're dead.