There are many reasons that the Carnegie Library of Pittsburgh and the various county libraries are not under one leadership. The first is that they are responsible to the people and communities who fund and use them. CLP is the system for the City of Pittsburgh. ACLA is an organization of libraries, but the libraries within it are often their own entities with only a main branch or one or two branches. The decisions for each of those libraries is made by their own library board.
EIN is a collaboration between the ACLA and CLP libraries to provide technology services to all the libraries in the county. EIN combines the libraries' buying power to get much better deals on Internet and technology services and computer leases. It also means that instead of every library having to employ IT and cataloging specialists, that is done via EIN. That said, there are some technological things that still need to be done in-house, so some of the larger libraries still require some IT staff of their own. (Oh my gosh, yes, an entity as large as CLP would require 5 IT people of its own. I don't think you realize how many computers and scanners and printers we're talking here, and EIN support is pretty much all off-site.)
Each library is a very unique beast, as is the community it serves. I'm a librarian at a suburban library, and I can tell you that the questions I am asked and the materials I buy differ significantly from what a friend of mine buys in Oakland, or another librarian buys up in Tarentum. Since the VAST majority of my library's funding comes from the local municipalities that fund my library, those local municipalities expect to exert more control over my library than, say, you. That is reasonable, I think. That's the model funding formulas were actually attempting to encourage in recent years--more local funding and interest in libraries.
Unfortunately, there are a number of areas that simply are too poor to support their libraries fairly this way, and there's also the City of Pittsburgh, which is the cheapest son of a gun I have EVER seen at funding its library. (I'm from a rural area in another state where the constantly-impoverished city of 30,000 there provides half of the funding that Pittsburgh does to its single library. Come on, Pittsburgh!) That's why RAD funding and state funding are so important. (Not that they aren't to my library--we squeeze every little dollar--but they are definitely moreso when they're pretty much the only money you're going to get.)
As for ACLA, CLP, and EIN doing the same thing, that's incredibly inaccurate. Libraries work with a lot of different organizations and also work together a lot. There are something like 43 different libraries in the county, plus all the CLP branches. My library alone ships over 1 million of our items every year to and from other libraries, plus checking out our own materials to our own patrons, putting on programs, answering reference questions, teaching computer skills, and providing meeting and study space. I go home at night and do more work that I couldn't fit in at work. So while the rank and file staff at the libraries handle all the day-to-day stuff, the directors handle running each library and coordinating, and ACLA handles coordinating the libraries and various programs that are non-library specific. They also handle some of the continuing education programs that all library staff are required to take (6-12 hours per year, depending on your position). CLP is huge enough and has its own funding and branch structures and needs that trying to combine it with the other libraries would be disastrous. (Having all the libraries work together and compromise to combine their holdings records into one catalog and work together under some basic rules in EIN has been stressful enough because there are some HUGE differences in needs and expectations between small libraries and large, and rural libraries and urban. Putting them under one roof will steamroll some section of the county's needs, just as people are concerned that the five branches that CLP is closing now are not necessarily the "fair" branches to close.)
As to the salaries listed for the Carnegie, I'll simply say that library staff themselves have found those interesting. What's also interesting is the dates that certain salaries shot up significantly (under the new director, some of them have practically doubled) as well as comparisons between salaries when two different genders have held the same position.
I should also add the qualification to this post that trying to explain library funding makes people cry. It's extremely complex, with each library having different revenue streams, and the state having certain budget requirements to receive state funds at all. Unless you actually sit down and talk to a director of a particular library, I don't promise you'll have that library's funding explanation correct. :P