In Path of Exile, at the end of every league they have two choices, roll it into the base game or remove it and use it as a rotating Zana mod. In general league mechanics tend to be fairly focused on a single mechanic that's isolated from the rest of the game, and as a result this choice is fairly straightforward.

I don't think Bestiary is that simple. The more I thought about it, the more I realized that there are all sorts of strange trade-offs to either choice. It's like Prophesy in that the mechanic is distributed throughout the game rather than being something that works in a single map, but it's also like Parandus in that it has a special currency that is useless anywhere else and like Rampage in that it changes the way we play the game.

If they keep Bestiary in the base game:

1. The league had a shaky launch, wasn't received well, and even with the fixes still has bugs. I've had fun with it, but overall perception of it doesn't seem great.

2. Beast crafting is extremely complex, adding a lot to the game that a new player would need to learn if they didn't play this league.

3. The mechanic strongly rewards certain types of builds and discourages others. Gameplay when trying to capture a beast is significantly different than the typical gameplay that PoE is good at. While this is fine for a temporary league because it's good to push people in different directions from time to time it's not generally what you're looking for in a permanent inclusion.

4. Crafting has a significant economic impact. Many of the recipes are actually quite powerful, and could have a major impact on the game if spawn rates of yellow/red beasts stay as high as they are. On the other hand, nearly all the worthwhile recipes also require very specific beast combinations so if the spawn rates are lowered then most players will never even complete them.

5. Nets add more inventory management and extra drops to pick up, not something the game is really lacking. With the exception of the necro net, balance of nets to beasts is way off. The different tiers don't add anything and once you're in late-game you get far more net drops than there are beasts worth capturing.