From what I've heard, Alph was actually the opposite case as Lucina, Dark Pit, and Dr. Mario where-in he was originally going to be a separate character and use Rock Pikmin but they ended up scrapping that and just made him an alternate costume instead.
Though considering Lucina, Dark Pit, Dr. Mario, and the Koopalings were all either originally or are alternate costumes, it wouldn't have been that odd..would you want them to just say 'Olimar' still?
My only guess is that either they weren't satisfied with his differences or Pikmin wasn't a popular enough series to split him off.
Sorry dude, but I disagree with you soo hard.
Adding 3rd Parties into Smash has actually enhanced the game for me and many others. Like, I absolutely love Nintendo and their games, but I, like many Nintendo fans, also like series outside of them..so adding in Sonic, Mega Man, Cloud, Joker, etc has been nothing but awesome to me.
If you want Nintendo only, there's Melee and 64 or you can purposely not unlock/purchase any 3rd Parties.
Not to mention Nintendo doesn't really produce that many successful new IPs..so bringing in 3rd Parties helps add a bit of freshness to it, even if the 3rd Parties included are from older games they're at least new to Smash.