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A few people on Newgrounds seem to think that Condition took too much from Cave Story.
How much did we copy, apart from the controls and basic weapons? I mean, all the brawlers on Newgrounds copy the same controls and attacks. All the brawlers share the same style. The same can be said about first person shooters, rogue-like games, RTSes, you name it, and they are still totally separate experiences. This game was build from scratch using flixel and drawn from scratch using photoshop.
Media isn't only about new things, it's also about self-reflection and interpretation of existing works. Keep in mind there are a substantial number of "cave story"-like games out there, most notably The Underside and IWBTG!.
And also keep in mind that you can compare other popular games to cave story. Look at Mega Man, Metroid, and Castlevania. They all share the same style pixel art, almost the same weapons, the same HUD, same controls, etc. Yet people consider them vastly different games.
Maybe it's just that this type of game is new to flash. Maybe once more of these games reach a finished state (And by visiting the Flixel.org forums, you'll just how many follow this run-and-gun genre) it will become more accepted.
In the mean time, I hope you have fun! That's all I was personally trying to accomplish with this game :)