I actualy think that the Tiberium from C&C 2 and 3 are of the same origin. That is, the Tiberium we see in 3 is actualy the same kind, but due to the fact that it extracts radioactive trace minerals from the source it's mutation has been accelerated, which eventualy lead to a stronger, more prevelant strain, which has most of it's biological structure interwoven with the crystals they extract. This would probably enable it to effectively use a larger part of the sun's energy, as well as the ambient radiation within the crystal as an energy source.
The disapearance of the Algea form is possibly due to massive suicide. Remember that the seas were litteraly covered in the algea. Such a large amount of biomass would extract all the oxygen in the water within minutes. A particulary hot summer night probably tiped the planet's reserve of tyberium algea over the edge, killing all of them and the entire nautical ecosystem with them. The seas are clear because they are completely and utterly devoid of any kind of life, in a similar way as how an algea bloom can masacre the ecosystem of a pond.
Note that if this is true, the world in C&C 3 also has some pretty damn nasty problems with global heating, since the death of so many algea produces huge amounts of methane gas (another killer for most aquatic life)