I do hate the wye. Especially the space between the CSX tracks and the NS tracks, directly behind the former Boylan Bridge Brewpub. That is about 5 wasted acres. Empire Properties owns some of it, but I would think that it would be nearly undevelopable, wedged between two active railroads and accessible only by at-grade crossings along Hargett on either side that are planned for eventual closure. The culprit is the NS line to Fuquay and its ridiculous diamond crossing the NCRR. Rip that out and build a sensible connection (as described in the thread) and all the problems are solved.
I would also like to see the parking lot inside the wye developed into an office building. There isn’t a lot of space to work with in there but there is some: the parking lot is about 15000 sq ft, which would be pretty typical for office building floor plates in Raleigh. Put a few levels of parking (some underground), go up 20 floors, and you’re all set. Call it Union Station Phase 3.