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Zynux
I wouldn't say Isaac's chances are "good" but I also wouldn't say they're "bad". He lands somewhere in the middle. His inclusion is definitely within the realm of possibility, and I personally believe he's more likely than... most remaining characters from unrepresented series (not all). I think people overlook the fact that in the past Sakurai has taken from series that have left the biggest impacts, even if the peak of the impact isn't exactly recent, such as Samus, Marth, and Ness. And while people like to act like GS has always been incredibly niche (as unfortunately is has gotten much more niche than it used to be), the first two games in the series did receive reception... roughly on par with the first two Pikmin games, and both Isaac and GS did have popularity worldwide. Ofc at this point it has become predominantly western-based (not solely western as some people think).
I think given Sakurai's apparent increased focus on originality Isaac's vast potential is a point in his favour, as is his enduring popularity, with even Dark Dawn at least keeping the series afloat in the few years prior to roster selection. Not to mention depending on how much Sakurai is drawing from results on the Brawl poll (as he did with Mega Man) it could be another benefit to Isaac, as he likely scored relatively well of the remaining characters yet to be playable. However that's only a possible boon, not anything definite.
On the other hand, GS's popularity in Japan has taken a rather harsh nosedive, and while requests for him are still intermittent, they are no where near what they were at one point. Sakurai isn't drawing solely from Japanese demand, but having popularity there would've definitely helped. Plus Dark Dawn's reception was fairly lukewarm and now GS has an unsure future, though that's not a nail in the coffin as far as his chances are concerned (though it's not good).
Given the amount of new series already added, and the ones still likely to be included (a retro, Mii, Pac-Man) Isaac very well might miss the boat again, imo it really comes down to how many new series Sakurai ends up including, because Isaac and GS are relatively high on the list of remaining series, but they're not at the top. He seems like the type of character that would just make it in Sakurai's initial wave of original (non-semi-clone) newcomers if he were to be included.
So... his chances are... ok. Not superb, but not horrible. I think a little better than most people give him credit for (I
personally see him as likelier than Shulk - but not by much - and most people don't), but it is quite a toss-up either way.