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I've played 3 Assassins Creed games briefly - I suck at them pretty bad so I never got very far into them.

I know what the Animus does, and it's an interesting idea, but I can't see why it does anything and IMHO it detracts from the story when you jump back from 1700's Havana to a modern office building to wander about a bit. I'd find the game more engaging if I was just the pirate/assassin rather than someone tapping into some kind of dream ancestry.

So am I missing something or is it really just pointless?

I personally have never understood it. I've only played a couple of games. I've always been very impressed by the immersive quality of the games and the time they put into their accurate depictions of the time the game is set.

Why then would they break that immersive quality with a boring side plot which just seems bizarre.

I've only finished Odyssey, but I didn't even complete all the DLCs for that.
I played maybe the first half of Valhalla, but lost interest.

The Animus sections are the single worst elements of both games and reaching those portions led to me quitting the game for weeks, months, forever, etc.
It adds absolutely nothing of value to the story and the gameplay of those sections is awful. Honestly, the only thing Odyssey and Valhalla really have going for the is the scenery and locales (so obviously Odyssey is superior). The overarching story isn't remotely interesting, it's a generic secret shadowy forces in a modern day urban fantasy are at war with each other over stuff. The individual game stories are slightly better, but nothing about them stands out.

The Animus bits are to remind us of the unreality of it all.

Sadly, I feel like those sections are typically written by another team.

Also, I think they could work better as cutscenes.

I never really got into the Animus side to the story in any of the games.

Some handle it better, even for the first game it was controversial a bit.
I like to think it adds some unique elements to the setting of the games as a whole. Rather than the games just being Historical Fiction.

I not sure they could remove it ether entirely from the franchise, honestly its a weird part in the series!

Loved Odyssey - the whole immersion into a quasi historic world and then there was the Animus - for me just a bit of tedium before we got back into the main plot.