Saffron City was a playable stage in the orignal Smash Bros., but did not appear in the sequel, Smash Bros. Melee. it was one of three stages that did not have a similar stage to it in Melee. although some people say that Fourside is similar, there are far too many differences.
Some of the Pokemon that appeared from the door in Saffron City, however, continued into Smash Bros. Melee, including Venusaur, Chansey, (back from the original game) and Electrode. it is also worht norting that although Porygon did not return, its evolved form, Proygon2, did appear as a Poke Ball Pokemon.