Adding a 5th trackway sounds nice, but....
There's only space for 4 tracks on the bridge. The main span has two outer portions on either side that might support subway cars, but the viaduct would need to be expanded. That wouldn't be a problem over randalls island, but in queens? Forget it. they'd have to bulldoze homes along the space that would soon be under the bridge, and if you think anyone is going to give up a half million dollar home in a centrally located low crime neighborhood without a fight, you're out of your mind. (to be fair though, at least here in astoria, I don't hear complaints about the occasional loud freight at night, etc. the bridge is pretty well accepted and even embraced by the 'hood, but any thought of expanding it would seriously not go over at all)
We're also talking about one long, long bridge viaduct here. I don't even want to estimate what it would cost to widen it. If I recall right, it cost them around $50 million in the mid 90's just to paint and maintain it imagine the cost of adding a track or two to the entire length of it?! We're talking billions here, easily.
I really don't even see CSX allowing passenger service on their track. Conrail struggled with the line back when LIRR was doing it's best to cut it's freight service at the throat in the 90s. CSX on the other hand has seen a decent upswing in traffic, enough to run 6 days a week, despite competing with CP, and NS via the cross harbor. Maybe, MAYBE they would do it if one of the commuter agencies upgraded the track for them, but then again, the line does have a decent grade on it, and there's enough occasions where they struggle to get the train up to the bridge. Factor in a little rain or snow, and stalling happens. Commuters potientally delayed, headaches... they'd have to add more power to the trains, which isn't high on their priority list I'd imagine (most common engines used are SD40's still in their conrail paint, not exactly the newest of the fleet...)
Despite all of amtrak's trains, they could squeeze in some commuter runs on their tracks, but only after LIRR gives up slots into penn station - IF that ever happens, even after ESA opens.
Running the freight at night? Try that and you'll get residents around Fresh Pond NIMBYing out of their heads. They already complain about NY&A... (though why they live by a yard is obviously a whole other arguement).