Omega was possibly a reference to this boss:

Dec 30, 2012 at 8:49 AM
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sOmega_zpsc439e810.png


From Strike Force Hydra (A very bad and mysterious GBA game. Few even know of its existence - all the better for them)



Either that or it's a major coincidence.
 
Dec 30, 2012 at 12:05 PM
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Hmm, you seem to have a point(either that or it's just a coincidence).
 
Dec 30, 2012 at 1:51 PM
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Its possible.
 
Dec 30, 2012 at 5:04 PM
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are we sure pixel even owned a GBA?
He's said a few times that his major influences were the famicom and super famicom, and I know he's mentioned having a DS but he like, kept it in the box or something because he didn't want to damage it :b

Double unlikely since the game you mention was released in 2003, and cave story was *finished* in 2004, and the Omega fight was presumably done a while before that.
 
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