It's not about rationally analyzing it. NCAA sports are a business. Business moves are not made rationally. They are made based on perception, personal relationships, timing (we got ed on this one) etc. There's also an assumption that the people making the decisions are smart, have all the necessary information, and have an incentive to make the absolute best decision. Unfortunately there are many irrational, ill informed, and lazy people running things.
a small part of the New York market is given more weight than the entire state of connecticut. I'm not saying that I agree with this, but apparently that is how the conferences view it.
IMPORTANT: Cable TV will drastically change over the next 10 years. The amount of households forced to pay for a conference network they don't want will plummet and the true value of teams will become more apparent. Netflix, amazon prime, some form of apple TV, some form of google chromecast, and other things that don't even exist now will completely disrupt the cable TV model over the next decade. 10+ years from now, owning not only all of connecticut, but also a good portion of NYC will be extremely important to the value of UConn's sports programs.
More people around the country would pay $50 per year to watch the UConn womens basketball team play on TV, than to watch Rutgers football. This fact will mean a lot in the not so distant future and some of these conferences will look back on this phase of realignment and see how stupid they were to base realignment decisions on the assumption that cable would continue to have a virtual monopoly on TV content and that households will continue to pay $100-200+ per month for mostly channels that they do not watch. If trends continue, let alone hit some sort of tipping point/ acceleration, than this model will completely change a lot sooner than most people think. Of course most conference commissioners will be retired by the time this happens so they don't really care, but it is not far away.