IMO, the routes are the same as we thought they were, back in the early 2000s when we were fighting JTA's original BRT plan, which was a lot more comparable to LRT than the current Skyway/U2C talk. We ended up with the First Coast Flyer and it's clear that this version of BRT-lite was everything we said it would be......which is regular bus service in a major city and not a replacement for LRT or a stimulator of TOD (despite the overselling by JTA back in the day).
To be honest, I don't know if building LRT from scratch makes sense with our low population density. You do LRT to connect DT with the Airport, Orange Park, Town Center, Beaches, etc., not just to hit a few neighborhoods immediately adjacent to downtown.
If we're talking streetcar, then scrap the U2C AV rolling stock and put a light weight streetcar or tram on the Skyway infrastructure for the starter segment and then extend at grade into Springfield (extend north through FSCJ's campus), Brooklyn (Riverside Av/Forest/Park to Five Points) and San Marco (elevate over FEC and drop to grade near Southern Grounds and Atlantic Blvd). The U2C Bay Street corridor thing screws up seamless connectivity to the stadium down Bay, so another alignment make make more sense there. Either way, we'd make this investment for quality of life sake and stimulating TOD to enhance our tax rolls and revitalize urban districts.
If we're talking something with reach to a larger population, the CSX A as a starter DMU line makes most sense. Yeah, you'd have to pay CSX A butt load of money (heck, it may be the same as the U2C the way AV estimates keep increasing), but you'd end up with something that could be operated like LRT and be supplemented intercity rail. That corridor would easily serve urban districts like Riverside, Murray Hill, etc., key employment destinations like NAS Jax and growing bedroom communities like Orange Park, Fleming Island and Palatka.
Intercity rail works better than other options on the FEC to me. The beaches and town center are so far away, that's a long term expansion project one some starter lines are up and running. If something ever does go to the beaches, the JTB corridor makes most sense. Going north, the S-Line is the easiest way to do it.