Yes, there are three Nintendo franchises left at this point with a notable fanbase that still lack playable characters in Smash Bros.:
1. Rhythm Heaven
2. Golden Sun
3. Advance/Famicom Wars
The first one was probably going to get a playable character (Chorus Men), but they probably fell into the same trap as the Ice Climbers.
The other two (especially the last one) have grim prospects of ever getting a playable character. Advance Wars has been in hiatus for nearly seven years, while Camelot seems like they don't even want to make another RPG, let alone another Golden Sun. Hopefully, as I said, Project M adds playable characters for these two series.
Also, I did not know the new Golden Sun track was simply a direct rip from Dark Dawn, as opposed to a new remix. It truly seems as though the series has taken a slide backwards in terms of representation in Smash Bros.
To be fair, Isaac's situation is at least better than Ridley (whom Sakurai has flat out come out as a Too Bigot). However, Ridley and Isaac are both characters that have had significant fanbases for Smash Bros. since 2001, and it is impressive that they have lasted as long. Hopefully, Project M will do what Sakurai probably will never.
I don't want to upset Isaac fans, but after Smash 4, I feel Isaac no longer has any shot at getting in Smash Bros. A Golden Sun character in general might be a possibility if a Golden Sun 4 is made, but by the time Smash 5 likely enters development Golden Sun will be close to 20 years old, and much of the fanbase will finally have moved on.
Its a shame Golden Sun received only a negligible amount of content in Smash Bros. in proportion to the following it has, but Smash 4 may have been the last opportunity for significant content to be included if Dark Dawn really is the last installment to the series.
The biggest hope there is for a Golden Sun 4 is the fact that Camelot does not really have anywhere else they can go for their next project aside from another RPG. They have lost so many employees during the Wii/DS generation that their output massively decreased (which is why they only ended up making a single Wii game and a single DS game during that entire generation). Their prime two staples, Mario Tennis and Mario Golf, have already had their new installments released for the 3DS, and as mentioned earlier, they are too small at this point to probably make a Wii U title. Their future looks cloudy, but if they want to make one more project for the 3DS, the only other skill they have in their book aside from golf and tennis games, is RPGs.
In general though, things look dire for a lot Nintendo's C-list franchises, not just Golden Sun. As mentioned earlier, Famicom/Advance Wars has been in hiatus for nearly seven years. Custom Robo has been in hiatus for eight years, and like Golden Sun, lost its Assist Trophy in Smash Bros. (and there is a decent chance that there is absolutely no Custom Robo content at all in Smash 4, while even in Melee this series received content). Starfy, while it retained its Assist Trophy, has not had a new game in about seven years as well (last installment was released only a few months after Brawl's release). Panel de Pon's last installment was a stripped down port released on DSiWare released nearly six years ago too, and nearly eight years since the last proper installment (Planet Puzzle League in 2007).
This is especially disconcerting considering how many of Smash 4's newcomers came from franchises entirely new to the playable roster. Punch-Out, Animal Crossing, Wii Fit, Xenoblade, and Mii's all received playable characters with this installment. Rhythm Heaven likely was too (especially considering how popular this franchise is in Japan).
For Smash 5, I am uncertain with what the direction will be considering that aside from Rhythm Heaven all other unrepped Nintendo franchises are inactive, and from veteran franchises the only notable names left are guys from the Mario universe,(Toad and Paper Mario), the DK duo (K. Rool and Dixie Kong), and possibly Bandanna Dee (Ridley is a very notable name, though unfortunately Sakurai has a strong opinion on him being added). From a guest standpoint, there are no third-party characters left on the same caliber as Sonic, Snake, Mega Man, and Pac-Man are.
Smash 5 might continue further down the road that Smash 4 did, which is allocate most of its newcomers to characters that were prominent in the epoch between previous and current Smash Bros. titles, but with their fading home console business and the cloudy horizons for the portable market, such new characters may end up being obscure even to the casual to the Nintendo fan set.
I think for Smash 5 there will be a new paradigm shift for the series. Smash 4 possibly took the series as far as it could go in terms of being primarily newcomer driven. With Smash 5, I can only imagine what direction will be taken.