Would be kind of cool to have them expand on the hacking skill tree. Include the ability to turn bots on each other (similar to the bezerk darts from Assassins creed)
Animals would be a cool edition (more than just the birds) to add a level of difficulty with the animals throwing off stealth, or a way to set up traps by tracking them and having the bots go after the animals while you pick them off. could even add some hunter tasks (idk, custom gear from hunting? craftables?)
and selfishly, as a primarily solo player, i would LOVE to find a dog in one of the abandoned towns (retriever?)or one of the bunkers (german shepherd?) and be able to have an animal companion.