Trilarion: Interesting. But does it make Cave Story a better game for it? I doubt it.
Was it really intentionally (and what was the intention behind) or was it just by accident?
In the case of the Nemesis, it is clearly intentional. If you level it up to level 3, your weapon will be shooting ducks. I think Pixel just wanted more variety, and wanted a weapon with a somewhat different playstyle. If it weren't for this unusual mechanic, the weapon would be too similar to your starting weapon, with the only difference being the graphics and the damage.
Of note, actually getting weapon experience requires you to pick up items that enemies drop, so if you can avoid picking up the items (or switch to a weapon that will appreciate the extra experience), you can avoid having that weapon level up. Also, don't forget that one hit and the weapon is back to level 1, making it powerful again.
Also, there are 2 areas in the game (one being the bonus dungeon) where your weapons are reduced to level 1 on entry; the Nemesis is definitely useful there.
dtgreene: For example, the game should be fair.
timppu: What is considered fair? Many (esp. free-2-play) games rely heavily on luck, e.g. Candy Crush Saga, Peggler etc. It isn't that much about you becoming good with the game, but you retrying a level as many times until you kinda get lucky.
Then there are games which are pretty much about trial and error. I'm sure there are more recent examples, but I'm thinking of e.g. a certain Amiga game,
The Three Musketeers (apparently there was also a DOS version).
As far as I recall, the only way you could advance in the game was trying different options handed to you. Some of them worked and progressed the story, some ended up in game over. It didn't have save game either, so if you failed, you had to start it from the beginning (which wasn't that bad as it was a short game IIRC).
Then again, maybe it was kind of a memorization game? You basically had to memorize which options were the right ones, and then you could finally finish the game. I think I finished the game that way, I wanted to know how it all ends (as if I wasn't already familiar with the story...).
Syobon Action feels like a memorization game when you actually play it (though there are a few parts where the execution gets a little tricky). However, that game at least offers check points.
I deliberately am choosing not to define "fair", but a reasonable criterion is that a fair game doesn't punish the player for making reasonable choices.