In my mind, armed with limited transit funding, i'd invest heavily in certain spots and not as much in others. Attempting to provide high frequency transit in areas of low density with no potential or desire to retrofit with higher density, is a waste of resources and everyone's time.
Instead, different environments should be allowed to develop and residents should have the choice of which they prefer to live and spent their time and money in. If you choose Argyle, that's cool. Just don't expect a train or bus to be out there every 15-30 minutes. If you chose Durkeeville, a denser built-up area with a transit dependent population where there's potential to double density with the right type of infrastructure, expect frequent transit.
With that said, I've grown to the point, where I'm not a fan of one transit mode fits all environments. Thus, in the urban core, given the landscape, river's position, costs of modes, street network, etc., I'd shoot for modern streetcar and the initial starter segment would be 5 to 10 miles tops. The more debatable question for me would be if it's better to leave the Skyway as is, or retrofit its infrastructure to accommodate an elevated streetcar that can then come down to grade to penetrate surrounding inner city neighborhoods.
If we're specifically talking LRT, and using a Houston model (a short starter segment that can't serve every area of town), given our landscape, the San Diego Trolley's Green Line would be a better example to follow.
I'd probably run with a starter that connects DT Jax to UNF via two straight lines. One being Kings Ave/Philips and the other being JTB. A 12 mile line would provide direct stops to DT Jax/Skyway system, San Marco, Philips Corridor (a great 6 mile stretch to rezone and essentially start over from scratch), Southpoint, St. Lukes Hospital, Deerwood Park, SJTC, and UNF.
This provides you with viable destinations at both end points (DT Jax/San Marco/UNF), and a good mix of high employment, medical centers, shopping, dining, multifamily that continues to mushroom along JTB and redevelopment opportunities in the middle. Unfortunately, you don't hit the Northbank, but I'm assuming the Skyway is still in place and that other opportunities such as modern streetcar, commuter rail, AAF, BRT, etc. come into play.
Future growth and funding leverages provides the opportunity for a straight shot to Mayo and Jax Beach. All those north/south and east/west arterials intersecting with Philips and JTB, then become perfect streets for high frequency bus service that we're currently calling BRT. The scenario I just described already exists in suburban San Diego where the Green Line serves a corridor just like JTB.