There was no need to change the structure of those agencies post 9/11. It's ultimately inconsequential whether FEMA has one more person in charge above it or whether the Secret Service reports to DHS or Treasury. These are huge bureaucracies and where you put them in the big organizational chart doesn't matter.
It was just one of those post 9/11 things. People had this "something has to be done!!" attitude. But, at this point, reshuffling those agencies again would be just as bad as doing it the first time.
I've heard differently. Supposedly the structure of the national security agencies pre-9/11 was so disorganized that some kind of overhaul was needed, thus the birth of the PATRIOT Act and Homeland Security Act. I'd argue that it was more incompetence on the part of those running said security agencies than the way they were composed, but nowadays the Homeland Security Agency seems to be in charge of the same crap the old, supposedly flawed, system was. The only difference between now and September 10th, 2001 is that now we're on the look out for smelly brown terrorists more than mentally ill white terrorists. But yes, you're right in that another reshuffling probably wouldn't create a better outcome.
