I do feel Y! did a great job -- and made a great decision -- in integrating its search acquisitions; but those acquisitions threw into sharp relief what Y! really was. It's hard to get into too much trouble when all you're doing is throwing horoscopes onto web pages; but Yahoo! never struck me as being serious about software, and as Paul says, they didn't seem to think that was a problem.
Somewhere in 2005-2006, Y! made an attempt to revamp its search ad services with a large-scale software project called Panama. It was going to do a lot of things, including ad ranking refinements to improve revenue per query, and allowing advertisers to create more complex ad campaigns. This project seemed to undergo huge troubles, and I wonder if it was ever completed in any real sense, because I heard so little about it, and everything I heard suggested disaster.
Honestly I don't know if the fruits of Panama -- such as improved auctions for ads on search result pages, which is a critical thing -- were ever deployed. But a couple years later they made the Microsoft deal. Over the last couple years, select people at Y! have moved on to Google, and many many others are now at Microsoft.