This to me is far more important than what animals get carried over/left out from PZ1 to PZ2, as the Franchise Gameplay aspect is why I play zoo games. So most of these are geared towards Franchise Mode:
1. Pathing System Fix - no more explanation needed
2. Overhaul to the "Animal Hitbox" to allow much better travel within an enclosure.
3. Hard Shelter update - I know I'm not the only one who puts a giant shelter into an enclosure - only to be told it's not enough somehow. This needs to be decreased. Also, for shy animals, add a "backstage" requirement that is completely hidden from the public(could be either a building like real zoos have, or could use natural items - foliage/rocks).
4. Random events - easily my favorite update. This should be a check box that the player could disable if they want. It would add disasters, like floods or fire, that would affect your zoo. Also, animal opportunities like housing animals rescued from circus/private owners, or taking in(whether permanent or temporary) animals from a zoo in financial trouble. That type of thing.
5. Conservation opportunities - rescuing and potentially rehabilitating local wild animals who are injured. Housing "problem animals". Add in challenges for your zoo to supply X number of a species for potential reintroduction.
6. Exhibit overhaul - additional sizes along with at least partial customization.
7. Change to Franchise Gameplay - Particularly the financial system. Current PZ is much too similar to a theme park. Guests shouldn't need to eat/drink/buy merch every 3 minutes. 1 restaurant, 2 food courts, 1-2 gift shops and the occasional vending stand are more than enough even for a good sized zoo. $$ should come mostly from guest donations, but also from prominent donors who will donate more money based on your "conservation rating" - which would increase with you having rarer species and participating in conservation activities.
8. Greatly increased education - Ambassador animals, animal-guest interactions, better petting zoo mechanics, and a wide range of educational props/activities. I was always a bit surprised that the base PZ game had so little of this, and it took a few years before the free updates began improving this by bits and pieces.
9. Make the Animal Market easier to navigate - also, I don't play Sandbox, but the idea that you don't have the option to find any type of animal with any stats you want is crazy to me.
There's a lot more I'm sure I could think of, but I don't want to bore y'all with a full on essay.