There were some major problems with the way intelligence was structured prior to 9/11. Some of them were fixed, and many new ones were created. (Well the second part is debatable, as most of the "problems" only exist for those concerned with civil liberties.)
The FBI is not really designed for preemptive missions. For the most part they investigate crimes that have been committed and prepare evidence for trials, much like a federal police force. That's not the best way to counter a terrorist threat unless we accept the commission of the acts as given and are content to prosecute after the fact. The thing is it's hard to design an agency that can be effective at both investigating crimes with a focus on prosecution, and at preemptively stopping major terrorist threats. The evidence procedures (among other things) needed to accomplish one of those missions are very different from what they need to be to be effective at the other. Whether that actually necessitated more alphabet soup is another matter, but there was a good reason to reorganize things.
I wouldn't say I have any real insight on the CIA/DNI/ASDFGHJKL thing that happened to the intelligence world so I won't comment on that. All I know is I have heard some reasons that sounded good on paper, assuming they were the whole story - which of course they weren't. Such is the world of intelligence...