After looking at the list of Classic NES Series ports that happened for the Game BOy advance, I can see at least a few potential retros that still has a chance unlike *sniff* *sniff* Balloon FIghter.
http://nintendo.wikia.com/wiki/Classic_NES_Series
If these games had received ports due to their cult status/popularity, then it's down to three potential series (Excite, Murasame Castle, Shin Onigashima, and Famicom Detective Club).
FDC had a crap load of remakes/ports ranging from the Super Nintendo to the Game Boy Advance and managed to make quite the impact in Japan. The original game itself was popular enough to spawn a sequel a year later, which is quite the feat. It did managed to get a few references in the series like an Ayumi trophy in Melee and a few Brawl material (Both Ayumi and Protagonists as stickers and a snippet of the second game's title in the Famicom Medly) over time. The game also had a slightly controversial live action commercial that promoted the game, which is still notorious even up to this day. The only thing that stops it from getting a character is the game's Japan-Only status and the fact that it hadn't had any form of reference since Brawl's release.
Shin Onigashima is considered one of Nintendo's earliest text based adventures back in the day (until the aforementioned Famicom Detective Club came along) and is still notorious up to this day for its high difficulty. It was popular enough to spawn a Super Nintendo remake that was compatible with Nintendo's Sateleview unit which had a few changes here and there. Like FDC, the series managed to get a trophy based on Donbe and Hikari and had some sticker representation in Brawl. The obvious difference when it came to music in Brawl was that it managed to get a full song/medley unlike FDC, which had a small snippet used for a medley. Though it still suffers from the issue of being Japan-Only, a character did get be reference in a post-Brawl game called Captain Rainbow (which is being referenced in Smash despite the game flopping). Chances are that Hikari may be a trophy against, but based on her CR appearance.
Next up is Excite series which has many things going for it like being a very popular series that had an international release and many sequels and/or spinoffs (Excite Truck and Excite Bike respectively) ever since. While it's debatable whether the series is considered retro or not, I'll still talk about ti regardless since it's a such a classic. It managed to have a 3D Classic and a WiiWare sequel (which was released a few years before the rise of the 3DS). Excitebiker was trophy in Melee (in which he was originally going to be fighter, but couldn't be added due to complications with jumping by bike) and appeared as a retro Assist Trophy that would attack other racers in a humorous race. Like FDC, a snippet of the game's title theme was used in the Famicom Medley track. While he MAY be considered as a fighter due to many circumstances, there's still the slight chance that he may return as an Assist Trophy since it appears that a majority of Brawl's Assist Trophies are slowly returning. Not to mention the series didn't manage to get a reference in Nintendo Land yet something as non-popular as Murasame Castle managed to get one for some odd reason (which will be explained later on).
Last but not least is non other than Murasame Castle and boy this one will be quite the doozie. Nintendo had really pushed the game to be popular in the past which included material like board games, guides that sometimes appeared in the form of manga, and a TV Drama (which was made to advertise the game at launch before Zelda's release, but got rescheduled along with the game due to production issues like film theft). But in the game, the game flopped and failed the garner the same success as Metroid and Zelda (also Kid Icarus to a less extent too) during the rough year of 1986. Despite this, the game itself had developet a small cult following in its home country that could explain the many things that would happen later. First, Murasame Castle was later ported to GBA on August 10, 2004 as part of the Famicom Mini Series like the previous classics I've mentioned so far.
Nazo no Murasame Jō is slated for release on the 3DS (which would eventually become the VC realese for the 3DS) and it was featured amongst other games from the NES and SNES to be released for the 3DS on a tech demo called
Classic Games at E3 2010. In terms of an odd cameo, the disk of the original Famicom title appeared in Pikmin 2 for no real reason whatsoever other than to be collectible treasure(which was the first reference to Murasame Castle that was shown to the Western public). Like Hikari, Takamaru himself also appeared in the game as supporting character quite some time after Brawl's release. A little while later came his rather unexpected appearance as guest character in the least popular Wii port of Samurai Warriors 3 (Murasame Castle's third time it was mentioned in an international game). While there could have been plenty of more famous characters to use for the game like Marth or Link, he must have been chosen due to fitting in with the game's style and for being a real samurai. Considering how huge the Warriors franchise was in Japan, it was quite the honor that such an obscure character even had the chance to play such a role. As for the series fourth mention in an international Nintendo title, it was none other than Nintendo Land. This basically raises the question of why this series got representation over the likes of Excite Bike and Mach Rider. It could be that the Big N themselves wanted to spread more awareness of the series to its Western audiences and they've wanted to throw the Murasame fans a bone over the lack of a sequel (which Kid Icarus managed to get due to being more successful than it in the past and Pit's lukewarm reception in Brawl).
Now for the Smash references: had little to no mention in Melee due to short development time despite the references of the other Famicom titles, sticker in Brawl, and a song based on the Overworld them in Brawl. Overall, Takamaru may or may not have a chance as a fighter (though the possibility of DLC is arguably higher due to limited roster space and lack or Murasame references so far) with the chances ranging from 40 -50% based on the cameos and ports alone. So far there was no mention of him being an Assist Trophy (which has a decent chance of happening depending on whether Sakurai wants new retro AT's or not) and there's still a possibility of him being a Captain Rainbow themed trophy. While Greninja appears as a
Big Lipped Alligator Moment! Japanese themed fighter, it's still a moot point since he originated from an international franchise and ninjas are no way related in samurai from a historical standpoint. There's still the Mii Shiruken issue, but there's still chance that his' can function differently since they could be more realistically sized and his throwing knifes are strictly forbidden due to the "no realistic gun/knifes" rule that Sakurai went by since Melee.
I could due an analysis for other retro Nintendo franchises like Mach Rider, but I only limited myself to the ones that had GBA port since plenty of research had to be done for such an analysis. While no retro could fall under the category of a "shoo-in" (Since barely anyone asked for G & W and R.O.B. and Pit had modest requests), there are a wide variety of characters to choose form and they have their own merits and their own flaws.