I see the culture of the two companies as incompatible. Yahoo! is a FreeBSD shop, they use lots of Free Software, MySQL, etc. Is Microsoft going to rip and replace all those servers? If they don't, they are saying FreeBSD and Free Software is better than Windows. I see this problem as being a very expensive issue.
Secondly, Microsoft has never borrowed money before to purchase a company. They were having Bear Stearns help them with this purchase, and while Bear Stearns is gone, they still will need some serious capital and will go into debt. This will change their culture, their ability to attract investors, and the bottom line.