Mandi "The MegaMaster" Paugh (The Mega Man Home Page) had this to say:

"Why did his hair change color? Well, technically, it's because they ran out of colors. The NES can only have 16 colors on the screen, and in the ending screen shot, it looks as though they are using all 16. Of course, this doesn't mean they couldn't have made an attempt to thunder up a color for his brown hair, or to give him green hair in the opening. Just a thought. =)"

René Boutin (sporeproductions.com) also had a great explaination:

"The explanation for the brown hair/green hair is sound, however another possible explanation is that the original release in Japan had green hair in both screens, since that's common in japanese animation and manga. When it was converted for US release, they probably had the hair color changed so it "made sense" to americans."

 

CHARACTER RECYCLING?

Several Sunsoft characters from BM appear in Sunsoft's other game, Fester's Quest. One of these characters is in the very first stage: the mutant frog (except it's smaller).

Its probably easier to recycle sprites and re-use them rather than draw new ones, but its more likely that the people who produced Blaster Master also designed Fester's Quest, and Sunsoft subsequently licensed Fester's Quest from that same company as well.

 

Some recycling examples:
 

 

 

 

 

METROIDS IN BLASTER MASTER?

This is just probably just coincidence, but one of the mutants from Stage 1 of Blaster Master looks an awful lot like a Metroid. All thats changed are the colors and the brain bits that are inside the real McCoys.

Its likely that the designers wanted to associate a monster that would probably exist in a water environment. The idea of a mutant jellyfish is just too appealing!