I can understand a reluctance to bring Isaac in as a fighter if it meant creating a new stage, which was probably low priority given 'Everyone is here'. But to then make him an Assist rather than hold out for DLC is a bit baffling if that's the case. So it probably points to them not caring enough about the character.
Unless he's still coming as the last one. ARMS got their character despite the Assist; there's a nice parallel there with the music still missing and second chance theory. But it's just as likely not true. He's still the most obvious first party choice Nintendo could make in my head, but I'm certain Nintendo doesn't think that way. I am at least convinced we are looking at a first party as the last pick, so my fingers are still crossed.
They didn't "make him an assist rather than hold out for DLC". Everything in base game was determined assuming DLC would not be occurring. This is red flag thinking that we know just isn't true based on ARMS and Xenoblade 2. ARMS got an assist and Xenoblade 2 got a mii, and both the assist and mii in both cases were the original intent for the playable DLC character. If they were "saving for DLC", those compensations would not have happened.
Sakurai has not saved anything for DLC whatsoever, and FP1 is a statement of that. That entire pass was all things that were nowhere in base game, while Pass 2, minus Steve, has all been things that had inclusion in base in at least some form.
Isaac being made an assist didn't happen because he's "out for DLC". It happened because we wanted him, but they couldn't yet do him. So he got the assist back instead, as well as the spirits, but no additional music. For ARMS, at best, it was chosen after the assist was added, but before the music selection was finalized. The music in the final game included **** as late as Mario Tennis Aces, mind.
Also, based on how ARMS and Xenoblade 2, both from 2017, were the ones chosen for fighter packs, but not more recent stuff like ring fit or astral chain, it seems clear to me that the pool of pass 2 characters was decided on quite early indeed. Remember, even if Heihachi's appearance in base was miniscule, it was still only done with permission.
So no, we're not likely to get Paper Mario, or Dragaux (why). And Waluigi has always had his own problems that have nothing to do with popularity.