It's not the compression since there was no such thing involved. I'd say it was moreso the transcription of the ideas to Game Boy hardware that sucked, specially the high pitches. Composition itself, as you said, was great. Just listen to a pitched down version of the tracks and you'll see.
In mega man 3 a block falls on Dr. Wily and Proto man was to late to save him and everyone thinks that he is dead but actually he survived somehow and starts controlling Dr. Cossack's mind and makes him seem like the next villain that "replaces" him and makes him create 8 robots to take over the world and when at the end of Cossack castle 4 you leave the Cossack catcher with 2 or less hp Proto man with Kalinka (Dr. Cossack's daughter) appear and she tells the truth to Mega man and then Dr. Wily reviles that he is alive and then of course Mega man deafeats him
