I came across a patch for Fire Red roms that includes data for all 649 Pokemon, as well as 4th and 5th gen moves. The patch only includes the data. It's meant as a base for rom hacks.
I then got in touch with the developer of the Gen 2/3 randomizer to see if he could edit it to include the 4th and 5th gen Pokemon. He did, and now we have a working randomizer for all 649 Pokemon. However, it is a bit buggy, and some Pokemon will cause the game to crash. I figure the more people we have playtesting it, the more bugs we'll catch.
Here's the link to the 649 patch: http://dl.dropbox.com/u/24219056/649%20Patch%20LB.ips
And here's the link to the randomizer: https://code.google.com/p/pokemon-randomiser/downloads/list
So please, patch up a Fire Red rom, randomize it, enjoy it, and report any bugs you come across.
UPDATE: Here's another mirror for the patch: http://www24.zippyshare.com/v/48039656/file.html