What are the best examples of growing pains that Google is now facing as it grows into a 100K+ employee company that are the same problems Microsoft faced 25 years ago?

I Joined Google after years at Microsoft, left a year later for a startup (Box, which is now no longer a startup :)). The Answer is very simple: performance review system. The engineering culture suffers when a developer’s compensation depends very little on the quality of a product and a LOT on how he/she performs compared to peers. Developers are much less likely to collaborate, more likely to compete, use meetings/email to intimidate and demonstrate their superiority, even claim credit for others’ ideas in a subtle way.