I would change an insane amount, Im going to follow the same character number limitations as sakurai. Note this is only if I had control from the beginning. Also characters in red boxes are unlockable.
First heres My N64 roster.
I would definitely have Bowser instead of yoshi since he is the main villain of the series and many would be excited to play with him the first time, yoshi would have been left at the wayside. Even though yoshi is important there are many other more deserving than him.
I would replace Jiggilypuff with Meowth since he is a way more iconic character to the pokemon world, he is known everywhere thanks to the anime he would be a permanent fit unlike Jigglypuff who was included on just popularity in japan.
Diddy Kong would replace ness since he was a more well known character (even though ness would be included later) diddy kong started in several dk games and had his own racing game around this time, it would be a great time for him to be included.
Captain Falcon would remain as the oddball of the all stars, even though F zero is an Iconic franchise this would be his first display out of the cockpit and would be used to show off how smash can give personality to certain nintendo characters and thers the fact a new f zero game for n64 would be out around this time.
Here is my Melee Roster.
13 Newcomers No Cuts
The six clone characters with only slightly different moves in this game would be Luigi, Dixie, Wolf, Young Link, King Dedede, and Ganondorf.
Dixie is another beloved kong in the dk series and the protagonist of two games, she would be an easy pick for a clone. She would be replacing Roy as a clone since she is more popular and important.
Wolf is Fox's rival and sometimes antagonist, he would be there instead of falco due to his extreme importance to the series.
King Dedede would be a heavy kirby clone in this iteration and woulnt focus on his hammer at this time, Id choose him over pichu since he is a very important character as Kirby's villian/rival while pichu isnt important at all.
Instead of Dr. Mario being a newcomer Wario (with his original Yellow suit ) would join with his various moves from the wario land series.
Banjo Kazooie would be joining due to their popular and well loved franchise, this character would be a testament to the history rareware made with nintendo.
Ness would be included as the first Retro character over the Ice Climbers In one way to appease Earthbound fans who were screwed over by the whole Earthbound 64 fiasco and another to show off a hidden gem of a franchise in the snes era.
Now time for what Brawls roster would look like
12 Newcomers No Cuts
One of the first priorities would be decloning
Several clones in the previous game like Luigi, Dixie, Ganondorf, Wolf, King Dedede, and Young Link would all be unlockable since they are basically new characters due to revamped movesets.
Young Link would remain in over toon link due to being more consistent to the series overall, he would be used to represent many of the zelda universe's other weapons.
Luigi, Wolf and King Dedede would all be decloned into what you see today.
Ganondorf would be a heavy magic/sword/melee user, would be a more complete character.
Dixie would play similar to diddy but have several unique moves like wolf.
Characters Missing/removed Here are Ike, Lucario, and Snake.
Lyn would be in over Ike due to her popularity and the fact she is the Westerns first Lord in the Fire Emblem universe and represents our first exposure to that games gameplay.
Lucario would not be in due to him not being iconic enough at the time or important enough to pokemon.
Red's pokemon would be Venasaur, Charizard and Blastoise since he is a pokemon master he would have all three of their final evolutions. Red's name would be included since he is iconic to the series in Pokemon Red, Blue, Gold, Silver and the comics. Red's gameplay would be alot more strategic than (meaning you will have reasons to switch pokemon) pokemon trainers gameplay.
Snake wouldnt be included since he honestly has nothing to do with nintendo at all, in a way his 3rd party replacement is none other than Banjo Kazooie, a deal with microsoft would be made to make sure the bear and bird return to still represent the history that they made on the nintendo world.
After melee's intro and the outcrys of tons of fans Ridley would be included as metroid main villain as a hidden character.
Little Mac would be included due to his popularity and his retro status, as well as the fact Punch out is a well established franchise, he would be the snes retro of this game. (Pit being the nes retro)
Tom Nook would be added to represent Nintendo's newer and successful franchise Animal Crossing, he is very Iconic to the game series since he basically owns your soul in the beginning portions of each game entry.
And at long last my Smash Brothers 4 roster
16 Newcomers No cuts
Characters Not included: Dark Pit, Greninja, Robin, Rosalina, Wii Fit Trainer, Shiek, Zero Suit Samus, Shulk, Lucina, and Villager.
Palutena is the only newcomer worthy of joining from Kid Icarus at this point in time, Dark Pit is a brand new and not very inspired character whose fanbase is minimal as well as his importance so he wouldnt be included.
Greninja isnt a very iconic pokemon and is relatively new so I probably would ignore him for Lucario whose popularity is still so high and maintened that he even has a huge role in mega evolutions and has been bumped up into an Iconic character, he would transform into Mega Lucario after taking so much damage at a certain point in the match.
Robin isnt included due to Chrom being the main character of Fire emblem awakening and due to the fact Chrom is more popular of a character. Chrom would receive a moveset simlar to what Ike would have had if he was included. Chrom earned his way in after Fire Emblem Awakening made a mark in history by saving the Fire Emblem franchise from certain doom.
Rosalina wouldnt be included due to her not being very important to the mario franchise and having a smaller fanbase than many other mario characters who werent included up until this point, Jr. would has become important and iconic as well as having popularity does a better job.
Wii Fit Trainer would never have been in the cards, Wii Fit would have received a stage at most (maybe, maybe at a later date I might think of this as a rep for like a smash game or two along the way)
Shiek isnt iconic to the zelda franchise or important, Impa on the other hand is a consistent character in the franchise who serves as zeldas protector, she is also cursed with reincarnation by demise, her moveset would function similar to shieks.
Zero Suit Samus wouldnt be something I would implement at this point in time since samus is always in her suit. Metroids two reps would be enough at the moment.
Shulk is from a new singular game niche franchise, Id consider his inclusion at a later date but for now he would be looked over.
Lucina wouldnt be included since chrom does a fine job at representing FE awakening, she could be a marth alt tho.
Villager wouldnt be included at this point in time, he may be your main protagonist but isnt much of a character due to being just a customizable avatar.
King K Rool would be added due to popular demand and the fact he is Donkey Kongs main villain.
Ice Climbers would be the Nes Retro character this time introducing the idea of a double character, DHD would be a lightgun history character.
Saki and Isaac would be two assist trophies from brawl evolved into full characters, Isaac who is popular and iconic to Golden Sun would represent camelot as well, and Saki would be the first N64 retro (even though SnP got a wii game) he would represent an old niche franchise and appeal to its japanese niche fanbase.
Black Shadow the Iconic/important and somewhat popular villain of the F Zero series would show up as a newcomer and take on attributes from ganondorfs old movset while retaining many unique moves of his own (think wolf ish). After this inclusion every series from the first game will at least have more than one rep.
At this pace there are still at least two games worth of newcomers worthy of being added.