Oh, but STATION SQUARE is not as isolated as one might think, diagonally across Smithfield and Carson Streets is one element of the connectivity with the urban core. Pittsburgh's amazing Light Rail system.
Seen from another direction, note that the LIGHT RAIL and the BRT system, one of the oldest in the country, share a stop at STATION SQUARE.
I'm sure there is a message in this for Jacksonville, now if our leaders could just figure out what it is. It's not enough to say we want Streetcars, Skyway and BRT, we have to ACT! If we had such systems, another giant parking garage wouldn't be eating more of our public dollars.
Oh my God, I was at Station Square when it was still a station! Pittsburgh and Lake Erie Railroad, an arm of the New York Central, that became Penn Central, that became Conrail, that became CSX.
To help your point, I'd like to add that the Mon Incline ties in with Station Square, offering service to residents of Mt Washington up the hill. While it may seem gimmicky or outdated, it IS a legitimate and well-used commuter resource. Plus its just o so cool.

I will concede that Station Square is one of the better developments of those listed (behind the Seaport and Faneuil Hall), but it is more a satellite than part of the urban area. Aside from those living at the top of Mt Washington, no one lives within walking distance (including downtown, which is largely empty at night). It has a ginormous parking garage, and the T station carries more park-and-ride commuters who park in the garage or the lot and take the T into downtown than it does suburban light-rail riders. The transportation infrastructure is great, but I don't think that makes the Square urban. And it and the T line are not as successful as we might hope to believe. Station Square is more dead than the Landing on a rainy/cold winter weekday night, and that's with much more diverse amenities than the Landing (river cruise ship fleet, BRT lines, light rail, incline, parking).
I think we can learn something from the Port Authority of Allegheny County (Pittsburgh's better version of JTA), but not from Station Square (unless its about preservation of historic buildings, in which case its a good study).
One thing that I think could be implemented by JTA (I'm assuming it hasn't been) is some kind of public transportation pass for college students. In Pittsburgh, the Port Authority has partnered with the universities to simplifying bus and T-line use. All you need to get on the bus or the T is a University ID (the university charges every student a Port Authority fee, but its pretty small and unnoticeable with tuition and all the other fees). This greatly simplified using public transportation for the students. You didn't have to think about fares or much planning of efficient routes, you could just go. That lack of planning had us exploring parts of the city that we may not have intended at times, but the simplicity really encouraged our use of buses. While buses may not be ideal at capturing choice riders, having a bunch of college students riding them really helps their attractiveness (I believe). Hence, many of my friends still in the city ride the bus to their fairly high-paying jobs. There is not as significant a stigma attached to buses there.
I would think it would be fairly easy for JTA to do this with UNF, JU, FSCJ, etc. I realize some of those are more commuter schools, but for a college kid without a car, the bus should be a great option.
This is a topic for another post, but your post made me think about it, so there ya go.