Speaking of atmosphere, I'll give an example of a truly great final boss fight, which is found in freeware game Iji. The music kicks ass, the whole thing has been built up quite well, the characters involved are interesting, the overall setting is just amazing for atmosphere, and the fight itself is actually fun with the boss having a variety of cool attacks to avoid, and an optional setting where he cranks the challenge up like crazy.
SPOILERS FOR IJI
Got to love that battlefield. The top of a ruined weapons research laboratory with a ruined city skyline in the distance (that the boss occasionally jumps onto to shoot at you) and the sky itself being red and filled with alien ships charging their weapons in preparation of completely destroying an already almost entirely dead Earth. Damn cool.
SPOILERS OVER
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Mistake you're making - overlooking the fact that we might not want to be saved.