1. Letting Lucile grow is required for a few of them. You'll get additional choices when you reach certain areas letting Lucile follow a path instead.
2. Corruption ending requires you to destroy everything. Make sure you destroy the first Village as soon as possible (it will trigger automatically when available) This one can be missed.
3. In the Lucile branches, there are some split choices, so save where you can to experience them all.
4. For the normal routes, you can just play as is.