It has everything to do with administration. When you have a chancellorship of a system, the universities below take orders from the one. This is entirely different from, say, PSU where the President of Penn State UP runs all the other campuses. Same way in Illinois.
I don't know enough about the Florida set-up to comment on it.
All I know for a fact is that SUNY duplicated the Cal-system in the 1960s, and--believe it or not--there are still people active and around from that era (the founding of the SUNY system) who know the institutional history like the back of their hands. The reputation of these universities were made by throwing huge gobs of money at the most talented faculty around. And they grabbed those people from the Ivies and the Cals.
Here's the definition of flagship according to The College Board :
“Flagship institutions are the best-known institutions in the state, were generally the first to be established, and are frequently the largest and most selective, as well as the most research-intensive public universities.”
Again - administration is a secondary factor and has nothing to do with the Flagship designation.
Per our favoraite source: http://en.wikipedia.org/wiki/Category:Flagship_universities_in_the_United_States
Interestingly, PSU is the only university on that list that is not a State University.
Upstarter, I understand the comparison you made above, but it is tough to compare PSU to other state university systems, because PSU is only state affiliated the same way Pitt is. Aside from PSU and Pitt, I do not know if any other university systems exist that have the same identity as these two (ie. State affiliated only, multiple branch campus, President or Chancellor of Main Campus controls branch campus). The Pennsylvania State System of Higher Education consists of 14 smaller universities and I can not speak for the administration structure of it.
We are talking about the importance of "Flagship Universities" with respect to conference realignment because when Jim Delany discusses B1G expansion he uses terms such as "Flagship University" and "Large Land Grant University". I think Jim Delany used the terms "Flagship University" and "Large Land Grant University" more as a metaphor than as a requirement. Per media reports, the B1G has considered GT and would consider VT and NC State if the acedemics were stronger. Schools like GT, VT, and NC State and large popular schools that are similar to Flagship Universities and clearly more valuable in realignment than any of the SUNY schools that you consider to be the flagship (Buffalo or Stony Brook). They are also more valuable than many Flagship Universities from smaller states.
At the end of the day, conference realignment is not going to be influenced by the technical identity of a university whether it be "Public, Private, or State Affiliated" or whether it be "Flagship, Land Grant, System, or Independent". Conferences will expand to include the universitities, public or private, that bring the most value to their individual conference whether it be monetary, education, location, etc.