I think they draw more from the games for Pokemon for one simple reason. Porygon appears in smash 64 as a stage object, and Porygon2 is a Pokeball Pokemon in Melee. A certain incident aside, the Porygon family doesn't exist in the anime.
Of course they draw things from both departments, but it's pretty obvious that the anime is the main source of inspiration. I don't even blame them for that, there's only so much you can draw from an RPG, considering how static they are in appearance. They also had to get really creative with Ness.
Couple issues here:
The most important one is that Pichu's self-damaging is canon. It's in the 'Dex.
Lucario's Aura thing was in the games, and (I believe) the perpendicular fur thing was described both in the 'Dex and shown in Battle Revolution, and his B-moves are all actual moves in the games. I believe there was a Dex entry that stated he was telepathic, but (and this goes for Mewtwo as well) the talking thing is essentially the same as the Pokespeak thing, since they don't say "Lucarioooooooo" or "Mew, Mewtwo" in the anime, it would be ridiculous to have them do so in Melee/Brawl.
It would be even more ridiculous to have them make canon noises when Pikachu and Jiggs don't.
Also, seriously, they're both telepathic, in the anime and the games.
Pichu didn't have any Dex entries before Melee that stated it hurt itself, closest is the Silver entry which states that it can startle itself by using electricity.
Lucario can only read auras according to its Dex entries, it doesn't fight with aura moves aside from Aura Sphere, and it doesn't become stronger from losing health either, though to be honest I'm not sure if it does that in the movie either since I haven't watched it. His B-moves are all actual moves in the games because the moves used in the anime are exactly just that too.
Also, I think X & Y pretty much established Lucario can't speak, so the telepathic excuse doesn't really cut it (and isn't stated in regards to Lucario in the games either.) Though to be fair of course X & Y wasn't out by the time Brawl was out. I can buy the Pokéspeak explanation in regards to Lucario and Mewtwo though, you're right that it'd be odd otherwise, but that still originated from the anime.