Of franchises already represented, definitely Yoshi, F-Zero, EarthBound/Mother, and Final Fantasy.
I see some people say Game & Watch but there isn't exactly many characters to implement into the game. Same goes for R.O.B. who is pretty much his own series.
More Punch-Out characters would be cool, like maybe King Hippo as another heavy, or Glass Joe just for laughs. But Little Mac represents the series well and I don't think we need more.
Yoshi only has Yoshi and there are a few good choices like Kamek and Poochy that would be welcome additions.
F-Zero only has Capt Falcon and Black Shadow would be a welcome addition (or any other F-Zero character but I would choose him first)
Mother has Lucas and Ness but a third like Ninten or someone more unique like Pokey/Porky would be great to see, though I say this with bias as Mother is my favorite series by far. Still, I think having another rep to either rep the one game in the trilogy that's not yet repped or the villain who would play completely differently than the two existing Mother reps.
Final Fantsay I know is a 3rd aprty franchise but the lack of care put into Cloud's addition is blatantly obvious for some reason. One character with many other great choices to add in, no spirits (seriously, none???), only 2 music tracks in his stage. Why even add him in the first place? Put in Cecil or Terra or Warrior of Light or Squall or Zidane or Vivi, or Tidus, or Sephiroth, you have so many options. Use them. Personally I'd love to see Vivi in the game because not only is FF9 my favorite in the franchise, Vivi is a beloved character and represents the series incredibly well just based on looks alone.
Other franchises I'd love to see repped...
Crash Bandicoot - Super obvious pick. It would be a crime for them not to include Crash into this.
Spyro the Dragon - Less likely but still would be super welcome to see.
No More Heroes - Travis Touchdown feels like a shoe-in. With NMH3 coming out (this year?) and a pretty heavy focus on Nintendo consoles, on top of that Travis would have plenty of awesome moves to show off, it surprises me he wasn't part of the first DLC pack.
Conker - Never going to happen but I'd die and main him instantly.
Pilotwings - So they have a Pilotwings based stage and an icon for it, and there are characters in Pilotwings, at least Pilotwings 64, maybe Lark from that game, and while it's not likely of Pilotwings getting a fighter, they could potentially give them some pretty cool moves, most of them based on flight.
Paper Mario - Okay so I know we have so many Mario reps as it is but Paper Mario would make a great new fighter because he would be different from just regular Mario and Dr Mario. Plus the series has a stage, and it's an awesome series (for the most part)