PSA (Penn Station Access) and IBX are indeed nice but missing some long neglected links. The alignment of the Hell Gate line is just so bad I guess (LONG curve and elevated sections) it is no wonder we never activated it fully with stations, though it should be possible.. It is a good opportunity to activate MNR and even LIRR if there was 1 more station passed Woodside for city commuters for example. IBX I read made Hell Gate incompatible due to the alleged 6 minute target headways, meaning the bridge doesn't have enough capacity for all service (Amtrak, freight, MNR). I don't recall if a full feasibility study for adding capacity was done. A Queens to Bronx connection would certainly be historic, and I think worth studying.