Obviously there is no way to know for sure, but this theory honestly holds up for me. The dates line up. The studio politics line up. David Yeats is there both times. According to Karen Gillian, Johnny Depp was attached to the Doctor Who movie - and if he *stayed* attached as it was retooled into Fantastic Beasts, that would help explain what is easily the most baffling casting decision in the whole franchise. Even people who liked Fantastic Beasts thought Johnny Depp was a bizarre Grindelwald. It is so obviously a role that wants a Colin Farrell or a Mads Mikkelsen.
Jacob is also SUCH a Doctor Who companion - normal guy, dead end job, swept away into magical adventures. He's really not a very JKR-ish character because... well... she doesn't write sympathetic muggles. Her muggle characters are villains, ridiculous (or both.) Or else exist totally off-page. Her most sympathetic muggle character is probably Frank Bryce - who is bad tempered, crotchety, and not very interesting. This is honestly kind of a structural problem: if your villain's main point is "wizards are better than muggles," I think you'd want to prove him wrong by writing muggle characters who don't suck.
But Doctor Who loves a normie protagonist who teaches the Doctor an important lesson about community, or responsibility, or love. That is 100% Jacob. There are also elements of Fantastic Beasts 1 that feel... pretty tonally off for a Harry Potter movie? I'm thinking specifically of the Death Cell execution room. That whole scene - the way it's designed and shot - it's all extremely horror movie. That's fine for Doctor Who, which has always had horror DNA. But Harry Potter doesn't. It also doesn't really make sense as a sanctioned government execution room, it makes sense as the sort of creepy, uncanny trap the Master would put the Doctor in. If Universal developed cool/expensive assets for Doctor Who, I think it's totally possible that they would be motivated to recycle them into Fantastic Beasts.
It also explains why Fantastic Beasts 2 (which would have been JKR's original work) immediately un-does a lot of the plot elements from Fantastic Beasts 1. The bittersweet moment of Jacob losing the memories of his adventure, but keeping his unlocked creativity and hope, that's such a Doctor Who ending. So is that moral-quandary moment of 'is there a way to stop this monster, who is both an danger to others and an innocent, without destroying it.' But in Fantastic Beasts 2, within the first ten minutes Jacob has his memory back and we hear that Credence is fine. Also... Jacob gets a wand in Fantastic Beasts 3. And it's not a "real wand" or whatever... but like, if the series continued, it was going to do something. (Because JKR doesn't like writing muggle protagonists.)
I will also say that in Fantastic Beasts 1 - information is delivered visually, film language is better understood, it has a good sense of its own scope. It's a filmmaker's movie, while Fantastic Beasts 2 is a writer's movie. It's got a million characters, tons of scenes of characters in a room or hallway just *talking* to each other (which is less interesting to watch than it is to read.) Important plot beats are delivered through monologs or extended flashback sequences. The pacing is much, much worse. The action sequences are much more confusing.
Okay. Fantastic Beats 1 could have been made out of assets originally developed for Doctor Who, and by some of the same creative team. Yeah. I see it.