Quote from RoboBlob:
It didn't make sense though. Why would a normal metroid, whose only weakness is ice, evolve into something that can be killed with missiles? Why were there no other metroid games with alphas and such? Why were there only 48 metroids on the entire planet? (including the queen, but not the larva) Why I asks! WHYYYYYYYYYYYYYYY!!!!!!!!!?
I've just been messing about on Fusion, and I think I came up with a new answer for this, one which makes a lot of sense.
Now, in Fusion, Samus gains a Metroids ability to absorb X parasites, right? Well, occasionally, when absorbing a big X, Samus will restore an old ability of her power suit. Why does this happen? Well, look at the attack forms of the enemies you get the suit's powers back from. To a certain degree, all of the enemies have powers similar to what Samus gets back from them. So, Samus is inheriting certain properties of the previous hosts of the X she absorbs. As for why she only inherits her old abilities, I'll say either she had the before, so it's easier for her suit to mutate into a form with those abilities and she'd have to absorb a hell of a lot of X to get anything new, or it's just plain coincidence.
Now, if a Metroid can absorb X in the sae fashon, maybe they can mutate in the sae fashon? I'm not sure exactly what creatures they're getting their new forms from, but there's a large enough variety of SR388 life that they're probably a mixture of different creatures. In my opinion, this certainly explains why evolved Metroids no longer seem to have the ability to drain Samus' energy and gain a weakness to conventional attacks: It's not in their nature to gain these new features, so they don't have to make sense.
This also explains why there are no evolved X anywhere else except the BSL station: its the only place Metroids are taken to that also has X in it. When the scientists were recreating the natural environment for Metroids, they were putting SR388 creatures in there, some of which were probably X hosts. It says nowhere in Fusion that the scientists knew why their methods of producing an Omega quickly worked, so it's easily possible for them to do it without realising X are involved.
The difference between Fusions Omega and the natural Omegas are that the Fusion Omega was grown very quickly, so it may have only absorbed the X that give it the appearance of an Omega, and not necessarily all of those that would give it an Omegas abilities. The fact that Samus can freeze its insides through the tough exterior can be attributed to the ice-plasma combo as stateed below, and the fight took place in a very cold environment, anyway: The hanger door was blown off, exposing the whole area to deep space.
Whoa, sorry for the long post! I thought I only posted a couple of short paragraphs. Anyway, I think I've covered everything that needs covering there.