The "future use" argument is something Sakurai hard said when deciding rosters, when explaining Smash 4.
It actually makes sense in this case why many were cut in that game, and why some don't appear in Ultimate. We wouldn't know Isaac was not playable till later on, which the only time one can look at that as a possible reason. No kidding it relates to hindsight. When else would anyone even think of it as a possible reason?
3rd Parties were never really noted in proper context with "future use" anyway. They got in on different merits unrelated to having future games. K. Rool has a very high chance of being in new games too, since the series is massively ongoing. In addition, 3rd parties are often highly iconic or part of a unique situation. Banjo & Kazooie got in due to massive ballot requests and their iconic nature. I love Isaac and all, but he's not part of the major icons either way.
Are we still going with this ridiculous idea of "winning the ballot"? Let it go. The ballot was nothing more than a suggestion box with tons of winners. Everybody that got something in Ultimate due to the ballot is an actual winner. Ridley absolutely got in due to the ballot. Calling it a secondary reason is silly. That's actually been stated as the primary reason he did so. It's because of that he had enough incentive to actually make a proper moveset, as "too big" and "makes more sense as a boss-like character" is why Sakurai didn't bother with him beforehand. We already know there's a lot who got in due to the ballot; both Belmonts, Ridley, King K. Rool, and some who are implied like Chrom and Dark Samus(Daisy pretty much can be thrown in here, since fan requests makes a lot of sense), and never mind it being a part of why Isabelle was an easy choice, due to massive fan requests due to her being a hyper popular mascot and a new gaming icon by that point.
Another example of a Banjo & Kazooie situation would be Sephiroth. They're both rather big gaming icons(though there's no denying you'll of course have people who never heard of them. They're the same level as Ryu and MegaMan. Fairly well known, but not massive in the same way Mario, Pac-Man, Sonic, and Steve are), and got in due to their own merits. Sephiroth may have even had a strong amount of requests, but we don't really know if that was related.