Both stories' common criticism was how obvious the mystery was, which is likely why it was changed in both films. I don't think the nature of the villains really mattered.
Doom is a broad strokes Tower of Babel adaption even if it's not an exact adaption (it's also one of the best JL films in my book, but that's another discussion).Crisis on Two Earths wasn't an adaptation. It was inspired by an existing story, but it wasn't in any way intended to be an adaptation of that story. It was based on a script by the late great McDuffie for the DCAU JL series. They didn't make those episodes, but thought the script was too good not to use. So you can't say they changed it, because it's not an adaptation. Likewise Doom wasn't intended to be an adaptation either, but it's also not a great movie and not worth the time discussing - it's just not intended as an adaptation of the Tower of Babel storyline, it only uses the Batman contingency against the JL idea.
Adaptional changes are always going to happen though, it just comes with the process. Nothing can be pegged towards a shared continuity mattering in terms of the choices made with adapting.There's more changed adaptations in the shared universe than outside of it. Maybe being a part of the shared universe was just a coincidence, but the numbers just aren't promising enough to say the universe sharing had nothing to do with it.
Doomsday was definitely an attempt to adapt the entirety of the Death of Superman saga within one movie. We just eventually got two films that were able to more closely follow the story.
Most of the UTRH changes were to condense and streamline the story and focus on the core aspect, which is usually why most adaptional changes happen.
I thought the shared universe had a fairly balanced track record with adaptions.Ignoring the original stories that take inspiration from the comics, and considering only real adaptations - the ones in the shared universe have the most changes that were also the most unneeded. The bulk of the rest can be explained by "not an adaptation" "trimmed stuff out for time" or "to work better as a standalone movie". The worst offenders happen to be Gotham by Gaslight, and the shared universe movies.