I don't get the Amtrak trashing. Amtrak runs an analogous service pretty effectively between Harrisburg and Philadelphia.
Top brass at the Authority wants nothing to do with Reading. This entire thing (Amtrak, the Schuylkill River PRA, etc) is only happening because SEPTA is worried that it will somehow impact the viability of KOP Rail, along with a general aversion to diesel, sharing trackage with freight, and logical expansion in general. The only trackage currently shared with a Class I is at Norristown, and that's being moved further west, almost eliminating it entirely.
You are right: SEPTA should be running to Reading. We retain trackage rights to Pottsville (though I'm not sure even our real estate department remembers). Our route is preferable to the proposed Amtrak routing (they plan on restoring the connection to CSX at ZOO and running via the RDG freight main) and could directly serve Center City with a one seat ride. Amtrak has trackage rights only as far as Suburban, not Jefferson or Temple.
Amtrak running the service isn't really that odd, however. They have plenty of comparable trains (Keystone, Hiawatha, etc) and would probably be able to throw more weight around with NS to get it happening. The direct ride to New York City (something that SEPTA is currently incapable of doing) is also a huge plus.
In a perfect world, the tracks between Cynwyd and Spring Mill would be restored and Amtrak would use that as access to 30th/Suburban, rather than the RDG freight main. It would keep them out of NS's hair until Norristown, and would be a quicker ride to Center City than even the current Manayunk/Norristown line. MAS on the Cynwyd is being raised to 40 mph in most places following the next resurfacing, and speeds could be even higher with a little work. This also opens up the door for a plethora of interesting ideas for SEPTA service patterns and reshuffling.