I hate to burst your collective bubble, but even if Penn Central hadn't been created in 1968 the PRR, NYC, and NYNH&H would cease still cease to exist today. All three, although very shaky financially, had prime routes that were coveted by other railroads. The PRR probably would have ended up with the N&W and the NYC probably would have ended up with the C&O. (Of course, that totally kills some of the other mergers of the last few decades and would have definately changed railroading as we know it today.) Given the course of things leading up to and after the Penn Central merger those would be the most logical conclusions.
Remember, too, that the original plan by the USRA called for two seperat federally funded railroads in the Northeast. The Penn Central was going to operate as it was and all the other smaller roads (E-L, CNJ, LV, Reading, PRSL) were to be merged together with one of the Penn Central lines to St. Louis. This would've created two competing systems in the Northeast and at the time given hope for future competition in the region. This plan failed, of course, when the E-L chose to remain independent and not be included in Conrail at first, only ending up in it at the last minute after its final bankruptcy.