Assuming the patched version is re-run from zero and the project includes the entire Solar system...
Downsize the star a bit. Make it an orange dwarf instead of a yellow one so it has a longer main sequence. With the right parameters, we could get 70 billion years out of it instead of 10.
Upsize the primary planet of interest a bit. Space travel will be more difficult for the inhabitants, but the increased mass should keep the planet geologically active longer to take advantage of the upgraded stellar lifespan.
Custom-craft Venus and Mars upgrades in vastly increase their habitability to give Earth-dwellers more attractive destinations for space travel. Possibly include basic life up to the anaerobic single-cell stage.
Set initial Earth conditions such that there are hundreds of small continents with large amounts of ocean between them shortly after intelligent humanoids have evolved. This setup should result in some significant speciation and by the time they start developing technologically there will be more variety available.
Include a 'second life' option - death of animals of sufficient mental complexity results in a spiritual existence with a similar span to the first life. Interaction with mortal existence is visual and sound only, no ability to interact physically beyond the minimum requirements to create sound and light. This may require the development of an entire spiritual realm with its own ecosystem.
Add 'auras' and have behavior influence them and have these auras detectable.
Leave a clear Earth AUP for sentient beings and kick any who refuse to accept it.