The special doesn't complete the Pokédex, it simply activates the National Pokédex. If you want to automatically capture every single Pokémon, well there really isn't a very efficient way of doing this other than a list of givepokemon commands. Note that this WILL make it seem like your game is frozen once you activate the script because of how long it takes to fully excecute. The best way to find out when it's finished is to apply the script to an NPC, interact with it, and then just hold down the speed-up button and a directional arrow key (so you know when the script is over as the player will start moving), you will eventually be released. This gives you Level 100 Pokémon from Bulbasaur to Deoxys. I made it using
this handy list generator. This requires XSE 1.1.1 and its accompanying stdpoke.rbh and stditems.rbh files, available
here.