There were some good ideas in the op, but the time frame thing seems like a complicated problem with no ideal solution. I agree that the pacing in the game makes one feel a bit more distant, and having a 200-year-old zoo is silly. And the rapid pace of the game makes it complex to articulate things like seasonal changes, weather, and those ridiculous alerts that an animal is too hot or too cold because the weather changed and it takes too long for them to finish their meal or even walk to the shelter.
But having it be a big deal to get to 5 years is problematic too, especially in franchise where the point is to get an economically self-sufficient zoo with a breeding program that is improving the genetics over generations. And having the babies grow up etc. is a fun part of the game too.
The problem is definitely the trade off between needing a time frame that allows years to pass in a reasonable time frame for breeding and income generation versus a time frame with the daily cycles and sort of real time behaviors of the animals and guests.
I'd like to see some improvements in animal behavior and biology to make them more realistic in some ways (fix the thing where chimps have the same social system as gorillas, for instance) and allowing players in franchise mode actually able to visit/tour one another's zoos in real time, maybe even opt in to chat with each other in game.
The conservation credits thing is, I think, an attempt to recreate the way zoos do business with one another, where the buying and selling of animals with money is actually not allowed.
Zoos and aquariums trade animals with one another, and there is a system where value of animals is calculated based on things like rarity, appeal etc. Having players trading directly with one another, via personal interactions, in franchise would probably be more realistic, but it could also make it harder for folks who play at times when few others are online or who aren't as good at networking (or prefer a more solitary play style). One reason I play franchise mode is that the animal trading is generally much better than in the offline modes where the only animals available are the frontier specimens, often very poor ones, or all one sex versus the other. And it's fun seeing the names other players give some of their animals and their zoos.