From my understanding:
A) Grades. The 63rd St tunnel under the East River is pretty deep, and getting trains from there up to even the existing lower level of GCT would require slopes that are unworkably steep.
B) Completely incompatible systems. Just about the only thing that Metro-North and the LIRR have in common from a technical standpoint is the use of standard gauge tracks. The elctrification systems are different, with MNR's being under-running 3rd rail and LIRR's being over-running 3rd rai. Signal systems are different, too, afaik.
In short, they don't and won't run together because it's physically impossible. Remember, though, that the ESA station being attached to Grand Central is an improvement over the idea of a fully seperate station from when the idea was first floated back during the 63rd St construction.
rails > roads
On second thought, let's not go to the NJ Transit Rail forum, 'tis a silly place.