I've been using a hori pad with A jump, B select item, Y shoot, X run, and Z cancel item. L and R at their defaults. Having the Z button so close to my right thumb is quite convenient, but practically anything is better than using the default of the select button for cycling through your items.
Also, I'm with Ian regarding story. It always makes me sad when developers foil their attempts at immersion with cutscenes. The Prime series is a perfect example. They go to all the trouble of having all these visor effects to make it feel like you're in Samus' suit of armor, only to throw it away every now and then by cutting to random, disembodied cutscenes.