They should've either focused solely on the animated universe they are carving with SPideverse

OR

Created a live-action film verse for a different version of Spiderman such as Spider-Man 2099 and the characters, villains and whoever else inhabits that universe. Its Spider-Man with a different twist and it doesn't muddy what the MCU is doing and allows Sony to have a complete ownership on their own Webhead

1. Don’t.

Let this sh*t die. Stick to video games, Marvel Studios making your movies or Lord and Miller producing them.

The villain spin-off universe was a stupid idea to begin with and I’m sure Feige doesn’t want these characters to cross over into the MCU. Sony should just let Marvel Studios make the live-action films and have Lord and Miller run the animated Spider-verse. If Kraven or Madame Web flop, I can see them putting this universe to rest.

My take is they should just get a writer/director and give him or her full control. Bet there is someone out there who genuinely wants to make a movie about certain villains.

I'm wasting my breath here, but...here's what I'd do:

Open the next Sony-verse movie with a flashback to No Way Home. Amidst the chaos of the final fight, we are taken to Toomes' prison cell. Scorpion approaches from the outside. He's free. Scorpion states "Peter Parker is Spider-Man" and watches for Toomes' reaction. Toomes turns away and walks back to his window. Scorpion gets louder: "Peter PARKER is Spider-Man. And your daughter's telling the magazines that they used to date. Two years ago. Right when you got caught."

This gets Toomes' attention. "Why don't you go ahead and say what's on your mind."

Scorpion (smiling): "Tell me you knew."

Toomes scoffs.

Scorpion: "Tell me you knew who he was...and did nothing."

Toomes (after a pause): "Yea. I knew."

Scorpion spits at Toomes, and Toomes walks back to his window. The shattering multiverse is seen in the sky. We hear Scorpion running off shouting "he knew! He knew allllllll along!"

Toomes (to himself, looking at the sky): "Of course I knew. I know everything."

He sees the sky closing up, and he mutters to himself more. "Peter Parker is Spider-Man. Peter Parker. Now everyone knows. Not my fault."

And then finally, as the sky seems to be fixed, Toomes says "be careful out there, Peter." And then, we hear people outside his cell questioning what he's doing there. We roll right into Toomes getting pulled into the Sony-verse, but we flesh it out a bit.

***

Now, we reveal that the Sony-verse is the Amazing Spider-Man universe (aka the universe in which Spider-Man stopped pulling his punches). With the Amazing Spider-Man returning to this universe, Toomes sets out on a mission to find him, as he feels Peter Parker is the connective tissue back into the MCU. But, as he hears that this Spider-Man is a "murderer", Toomes decides to build a team to take him on. This is the Sony-verse sinister six. Vulture, Morbius, Venom, Kraven (sigh), Electro (he was never totally "fixed") and an improved Rhino.

And of course Madame Web is the multiversal force that's able to pull Tobey and Tom into the Amazing universe for a cameo at the end of their sinister six film.