The convention center needs to be doubled in size. The exhibition hall is only 78,500sf. Cutting it down isn't the way to go if Jax wants to be in the business. Either expanding it or building a larger center off-site are the options for remaining in that industry.
In either scenario, whether the convention center stays or goes, the potential location of Amtrak platforms and the existing Skyway station remain the same, so you're not gaining much by tearing down the exhibition hall and moving the intercity terminal there. At least utilizing the existing Skyway bus bays for the intercity terminal, allows for quick short term implementation at an affordable price. Given that the Skyway and intercity buses are local, it also makes sense for transferring between those modes to be as efficient as possible.
Nevertheless, the bull in the china shop situation is still COJ coming up with a solution and cash to do something with the convention center. That's not happening anytime soon, so is it worth not doing anything to improve intermodal connectivity, while waiting on a resolution for the convention center that could never come? Furthermore, in the event that AAF does eventually expand into Jax, then we're presented with another opportunity.
It would be cool to have alternatives for if the convention center stays and expands west, or goes altogether. My guess is that you'll find parts of the layout that won't really change one way or the other. In a phased implementation plan, that's where it would make most sense to invest first. In that scenario, I think intercity buses directly under the Skyway makes sense.