They should just give us an extensive color edit mode like King of Fighters so everyone can have whatever color flame they want and I can make mine Green because screw everything. And just think of all the fun of color editing MR. Game and watch!
In all seriousness though, the Red fFame makes sense to me. What I've constantly heard from lots of different people(though I've never seen a source given so I don't know for sure if it's speculation or something Sakurai actually said, but either way it's a fair assumption) is that Eruption isn't meant to be a reference to the end of RD where Ike strikes down the goddess, but rather a homage to Roy, and the reason it was red all along with is presumably because Roy has red flames (I mean it's not like RD wasn't already out when Brawl was made anyway). In fact according to what people say(again, I've never seen the source) Ike wasn't originally planed to have eruption at all, he was going to have Ragnel's projectile attack but Sakurai changed it last minute because A. balance and B. It became apparent Roy wasn't going to make it. Assuming Roy again didn't make the cut, changing that attack in any way could be seen as spitting on Roy's grave, and Sakurai has already mentioned he feels bad about hurting the fans of cut characters.
Also, why is Ike called the Hero of Blue Flames? He uses them once ever at the very end of his story and barely anyone was around to see it and the visual representation of which wasn't particularly significant anyway. I didn't even understand why he had blue flames in project M until I replayed RD and I was like "oh yeah, that happened. I forgot about that". He could be like the Mercenary General or the Hero from Gallia or the Hero of the Golden Sword/Wind Sword/Ragnel/Aethier Yune's Hero The Unifying Hero ect. ect. just the Hero of Blue Flames really? I guess it sounds cool?