Easy fix, though 8) Just change it a bit...
For example, instead of a jetpack, use wings.. Change the textures a bit. This can be done quickly and easily using even Photoshop. Just filter the main character to different colors, add wings, make the arms a bit longer, and you no longer have the Metroid character.
For levels, it's even easier. Unless your map is a clone of one of Nintendo's maps (in which case the whole map would need to be scrapped), all you have to do is alter textures a bit, so they don't resemble the ones in Metroid.
For sounds, just find a sound which could be used instead of the one you have. To keep up with my jetpack example, the sound of a jetpack going off can come from alot of places: start a car, flush a toilet, set off firecrackers, buy a jetpack and record the actual sound (lol).
Once you do those two things, rename the enemies, weapons, main character, and the game itself. Once all copyrighted info has been changed, release it 8)
Include in your End User Liscence Agreement that you were inspired and influenced as a budding developer by Nintendo's earlier works. Also state that the game is intended to be similar to Metroid, but not the same. State that if anyone finds any specific content (texture, sound, model, etc) that is too similar to one of Nintendo's that it will be replaced, and the new version will be distributed.
Doing these things may still get Nintendo's attention, but in court you could prove you were not copying Metroid (unless Nintendo happens to visit this forum lol).
All in all, Metroid is such a classic game, it is nearly its own genre. Consider all the centipede clones out there! They all are the same basic concept as the original, but the author added something to make the gameplay unique.
I would recomend adding to the game a bit. It helps to say, should the worse happen, and you do go to court, that you don't include in your game what they included in theirs. It also helps to say that you do include in your game things they didn't include in theirs. If you can show and prove both of those things to enough of an extent, they will have no case at all, because you will have a unique piece of work 8)