It looked like them. I'll explain it more in-depth.
Someone else generated 3 random pokemon. They then went into the game's files and replaced Treecko's, Torchic's, and Mudkip's models and animations with those three Pokemon's. Their names were changed from Treecko, Torchic and Mudkip to Darumaka, Togepi and Tynamo in the text files. They were generated random moves and abilities, but in essence, they were still Treecko, Torchic and Mudkip. For the first battle, he used what was essentially a Treecko. After that, there was a cut in the recording that the audience wasn't allowed to see. His save was extracted and edited so that he had an actual Darumaka instead of a Treecko, and it was probably at this point that the starters were un-model-swapped and their names were reverted, then the ROM was rebuilt, he injected his (modified) save, and continued the game with his 'randomised' starter on that new ROM.
The reason that wasn't shown, though, along with a bunch of other cuts, was simply for the sake of the viewer's entertainment. Yeah, it kills a little bit of the magic to know this, but there's no current way to do what he did except for what I just said (or a slight variation thereof). Sorry.
I can PM you the latest version I've built, or you can try to build your own using SharpDevelop. I know that you might wanna use Visual Studio Express, but I've been using SharpDevelop and it's been just fine.