Megaman Anniversary Collection doesn't support 480p, so there's no point in changing it to progressive scan (if you even can with MMAC). Just using GCN's component cables make the game look so much clearer and crisper compared to other connections. Afterall, better connection, better quality.
Though are you using the GCN component cables that plug into the D-terminal or component cables that plug into the generic A/V slot (if there is one)? Or it could just be your settings (afterall Pikmin 2 is a pretty bright game) so try that. Or get better eyes.
And for pure eye candy, go to a Best Buy or Circuit City (or any store with HD TVs), ask a sales associate if you can bring your GC to test out one of their TVs (a good one that supports 480p especially). Hook it up, put in F-Zero GX, enable progressive scan mode and prepare for pure eye sex.