No, no, no!
In the recent edition of Nintendo Dream in Japan, Gamefreak (Pokemon's developers) were interviewed, and they said that in Summer 2003 in Japan, a new Pokemon game for GAMECUBE will be released, and it'll let you get your old Pokemon.
Since all the data for the "unobtainable" Pokemon is in Ruby and Sapphire (ALL 386 Pokemon), it makes sense.
When I say data, I mean stats, abilities, characterisitcs, sprites, EVERYTHING that an obtainable Pokemon has. So no worries, people! There were problems with compatibility between old version of Pokemon and Pokemon RS, so backwards trading wasn't possible, but no doubt the old Pokemon will be obtained by sticking your old versions of Pokemon into the Gameboy Player in the Gamecube while the new Pokemon game is in, and then withdrawing them into the GC's Pokemon PC, and then sending them to Ruby or Sapphire! ^_^