<i>This whole process would be a lot simpler if we just went with one completely national body for passenger rail.</i>
Maybe. I don't see it as an answer, and 30 years of Amtrak is a good reason to believe it wouldn't be.
<i>Let Amtrak run everything, Commuter or Intercity, NJT, SEPTA, MBTA, MN, LIRR, Metra, Metrolink, Sounder, whatever, if they run a train which recieves public monies, give it to Amtrak.</i>
Ugh, no. NY area transit agencies are already non responsive enough. Putting management in DC and putting them at the whim of congress would only make it WORSE. And, it would lead to the same lowest common denominatorism that's plagued Amtrak for 30 years. They can't see any 'solution' that doesn't involve Superliners or Acelas or Amfleets. They refuse to innovate (where's the DMUs they tested a decade ago, to rave reviews?), they can't manage projects right (numerous GAO on NEC reports, among others), and they have zero direction. At least now you've got a few agencies that can look past the F-40+4 bilevels crap that's made commuter rail in the US a laughing joke (Oh wow!!! 3 trains a day to chose from that are no faster than driving, and it only cost us 100 million to build!!!)
I could imagine Septa's RRD under Amtrak control. Two Cali cars sandwiched between 2 P-42s, running even slower schedules than now at a higher cost. But it's <b>standardized</b>!!!
Given how much Amtrak's fought with NY state about running the turboliners, do you really think they'd offer anything better than a loco plus 4 bilevels for commuter service? There's lots of places that are poster chldren for DMU, or even EMU operation Gunn talks a slick talk about the need for DMUs. Amtrak has exactly zero on order, and plans to buy a dozen 'in the future' for one line in CT. Amtrak's been 'experimenting' with DMUs in various services for years now (remember the Flexiliners on the early 90's?), and talking about it since day one (Big effort was the horrid SPVs which were a disaster from day one, and the result of NIH rearing it's ugly head - They couldn't have looked at what worked? No, design it with a clean sheet of paper and pray.)
On the other hand, there's at least 2 current active DMU orders of two different types at two different agencies, and a LOT of others standing on the sidelines ready to look at the results and maybe jump in. There's talk of electrifying lines out west. Heck, even Metra, as backwards and stuck in the 50's as they are, has floated the idea of DMU based services (amazing! a train that's not slow, smelly, and can actually brake and accelerate!)
As little as it is, the innovation in the US is happening at state run agencies, NOT at the federal level, where the biggest showing of the FRA/US DOT/Amtrak so far has been a 1/2 assed Acela project, a helicopter engine in a locomotive (because it worked so well the first dozen times it's been tried), a single line 'experiment' in implementing PTC, which is desperately needed in the US, and a lot of talk.
Yeah, the existing setup sucks, no doubt. But rolling it into Amtrak will just give Amtrak even less direction (if that's possible) and result in worse service overall, and kill any chance of making progress w.r.t. passenger rail.
It'd turn into a finacial hairball, too. I just don't see how putting it all under Amtrak would help anything - they can barely run their own trains as it is.