One of the biggest questions that always surrounded Metroid Prime: Trilogy was how they fit two GameCube games and a full Wii game onto one disc. Keep in mind that extra data was also needed to program in the new controls for the two GameCube games so the question of space management becomes even more extreme.
It seems that part of the answer may be that corners were cut in other ways. As you can see from the video above, the Wii version of Metroid Prime, when compared to the GameCube version, is missing some graphical effects. Most notably, some water rippling effects are gone, as is the condensation that gathers around the mouth of the Ice Beam when it charges up.
Some also noticed in videos for the Japanese versions of Metroid Prime 1 and 2 for the Wii, which were released as separate games, also had these graphical pull-backs. While this may cause a storm of “Wii is not as powerful as GameCube” jokes, a more rational (but completely speculative) explanation may be that they were programmed for their inclusion into Trilogy first. Then, for whatever reason, Nintendo decided to release the first two Primes on their own, as part of the Japanese line of the New Play Control series. Instead of starting over from square one, they just took the code from the Trilogy version and broke it back into the separate games.
If this is true or not, however, does not change the fact that these minor changes are there and while it may disappoint some, it does not seem enough to take away from the overall experience.
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