Loading time differences between various ports of the game are something that have come to my attention recently. Here are some ground rules and some other notes:
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Emulators tend to load faster. For anyone trying to competitive speedrun, we endorse using an emulator.
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Any settings in an emulator that otherwise speed up loading screens are banned (such as PCSX2's Fast CDVD hack).
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Newer versions of Dolphin (Gamecube emulator) have slower loading screens. The newest versions (as of writing this) have loading screens that are roughly 1-2 seconds slower. We recommend using the original 5.0 release of Dolphin if you are looking to get a competitive speedrun.
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In a test I did years ago, Dolphin and PCSX2 seemed to have very similar loading times. I redid this test recently (in a limited fashion) and it seems Dolphin was faster. I will have to do further testing on this.