Curate, connect, and discover
(and Thad, but shh)
Instead of Bart being saved and sent to the past by Meloni and Iris, he instead stays in the future and under the rule of President Thawne.
He is then basically groomed and made into a super-soldier/mercenary for the government along side Thad (who is Barts' twin and not a clone). The two grow up in VR together and the simulation basically trained them to be said soldiers.
Then they two get sent back in time by President Thawne to kill Wally - who is their father, because we don't have Barry.
In the end, the two have a redemption arc and end up helping Wally while still having the skills and mindset of children who were groomed into soldiers.
Pure autism bellow;
The reason Bart and Thad grow up together in VR is to create a sense of only having each other. They won't be loyal to Thawne, only to each other simply because they are the only ones they've ever known. The lack of human contact in Barts' backstory always seemed weird to me, since it wasn't really explored, so having the two of them will allow them to still have the sense of humanity.
The ageing problem: For those unaware, Bart experienced rapid ageing dur to the speed force and was only able to start ageing normally when Wally fixed him. This gets changed to the scientist fixing them, but after a longer time - so Bart and Thad are both ~15-16 when they go to the past instead of being 12-15.
Wally being their dad is so they have more of a connection (also I think It'd be really cool if Wally didn't know and Bart and Thad used it against him once he found out). Also because, again, there is no Barry.
Lastly, the whole VR thing. I always found it weird that the VR was like a weird game/fever dream. Like, why would the government spend so much money and time on a child to get nothing out of it? So, having the VR actually be more similar to something like Elden Ring or Skyrim where it's opened world and they can talk to whoever - but they have to fight a bunch of big bads. It'll also be really intreating to explore the lack of care for other human life because they wouldn't realise that people aren't just code until later. (murder twins, and when Wally gets mad at them they get confused because they simply don't understand)
Uhhh... yeah. Bart and Thad being brother and child soldiers for the government sent back in time to kill their father is something I'd like to see.
(I just want to explore the consequences of children being raised in VR and not being socially conditioned properly... man, I have issues).
this is the baby they insisted was a threat :(