There are actually just 2-3 choices that determine your route, everything else is basically just a choice between "show content" and "skip content" and doesn't have any meaningful impact (except for Wife's Job branch, where you have to chose if continue this branch or quit her job and start the "MC's companie" branch which i wouldn't recommend since the Wife's Job #1 branch's progress is required to get further into the Wife+Jenna branch, dev made some adjustments but the "Wife+MC's company" branch is mostly pantyhose fetish)
Add Wife + gym NTR off -> Alpha Route with Wife, Paul(a) branch and Niece romance branch, Hearth/Kirely/Sola branches
Add Wife + gym NTR on -> Cuck Route with Wife (most content), FemMC branches, No Niece #2 branch even after adding her to the app through the Wife+Paul choice, future Wife+Paul content possible on how the branch ends (to get to the newly added v0.5.0 FemMC content you've to refuse to Paul's deal when he requests the MC's wife and her sister)
no Add Wife + gym NTR off -> Alpha Route (Wife gets added to the MC's app later on), Paul(a) branch and Niece romance branch, Hearth/Kirely/Sola branches
no Add Wife + gym NTR on + MC Cuck branch step 6 "Sissy" -> Sissy Route, default Niece BBC branch, no XY App content
no Add Wife + gym NTR on + MC Cuck branch step 6 "Cuck"(w/o sissy tag) -> Cuck Route (netorare/netorase route later on), FemMC branches (leads into Niece BBC branch at the very end before content ends, future FemMc+Niece+Paul content possible on how it ends, Wife+Paul option to save her stops working at step 113 since you don't have access to the Wife's phone)
(to get to the newly added v0.5.0 FemMC content you've to refuse to Paul's deal when he requests the MC's wife and her sister)
"no Add Wife's Sister" content only works with the "no Add Wife" route since it requires "Wife not added step 48" to trigger.
Even after adding her to the MC's app shortly after in the noAddWife Alpha Route her "MC+Wife's Sister" branch doesn't show up, so no point in not adding her when going for the "gym NTR off" option for that route.
edit: slightly updated.