Isa could replace Saki to make it more modern. Other than that, your roster's nice and realistic but it's bit too tame for my taste. Where are the more outlandish inclusions, like Square-Enix characters?
Was Black Shadow included just to keep Ganondorf's clone moveset in the game? He's a blander character than Waluigi. If there's room for another F-Zero character, don't you think that one of the OGs like Samurai Goroh would be a better pick?
Thank you for your compliment.
Anyway, in regards to your questions,
I picked Saki over Isa because Saki is far more popular than Isa (and besides S&P2 bombed harder than even the original).
I was actually contemplating a more "out there" character to place in such as Duck Hunt Dog or Lip. However, I opted for more conservative choices I guess. I was thinking about possibly switching out Toad for Paper Mario too. If I brought in Duck Hunt Dog or Lip, I would probably switch them with either Starfy or Saki.
For third-party characters, considering the only third-party character that is widely desired is Mega Man, he was the only one I added. Smash Bros. is first and foremost a collection of Nintendo characters. For Square-Enix, I don't think there are any characters that really stick out to me or would draw people to the game like Snake, Sonic, and Mega Man would. Maybe Cloud would build hype, however, he has never have a prominent appearance on a Nintendo console (outside of small cameos in Kingdom Hearts games and I think he will be appearing in Theatrhtthym Final Fantasy). There have been people who have suggested Slime, however, I am not sure exactly how the character would go over, even in Japan.
In regards to the F-Zero character, yes, the main reason I chose Black Shadow over Samurai Goroh because he could easily take Ganondorf's old moveset. Black Shadow is a very important character to F-Zero though, Captain Falcon's arch-nemesis. For Samurai Goroh, I also assessed that there was little to base a possible moveset for him on, and that Takamaru was already in to give the Japanese katana swordplay style. If there is a newcomer for F-Zero added, it will either be Black Shadow or Samurai Goroh. I think the F-Zero anime does make one also appreciate Black Shadow a bit more (he is voiced by Norio Wakamoto in it). On that note, I remember reading a few years ago prior to Brawl, that Wakamoto would be glad to reprise his role as Black Shadow for Smash Bros. if he was asked to.