At Washington the most common delays northbound seem to be track signal failures, such as between WAS and BAL. Has happened several times in the past few years, and it cascades immediately. I don't recall if that segment is on the official list of backlog projects, which are finally getting some funding. People seem to focus on speed improvements, but you could say that's a less important side effect of clearing up the capital backlog.
The most common delays southbound from WAS are freight interference and failing P42 locomotives. I wouldn't expect any improvements in freight interference beyond Virginia and North Carolina, and meanwhile freight traffic will increase. The P42's are being replaced by Siemens Chargers. The Autotrain has a small pool of Dash-8 locomotives to fill in for bad P42's.
One note on Amtrak's financing, as an example, about a decade ago the federal government sold the massive air rights from WAS station over the platforms to H Street. Measuring with my finger, that's about nine acres. It starts 50 feet up, so there is still room for the planned concourse to H Street. Amtrak needed the money.
As for management, the key is transparency, and there are few journalists really pushing Amtrak on this. In other words, the Transit Costs Project at NYU has the right idea. The researchers had to become reporters, finding sources and scouring obscure public documents. It wasn't about Amtrak, but there's a similar tendency to insularity (contracts are proprietary!), and negativity from many observers. Even the press releases from Amtrak have a different tone nowadays, focusing on fixes rather than fluff, such as the wonderful cartoon poster at Washington Union, of Jane Pauley and Briant Gumbel riding the "Today Show Express" in 1985.
Inside the WAS station, there's a 99-year lease on most of the available space, and Amtrak is admirably fighting to break it. The leaseholder proved inept at WAS and worse elsewhere, with the lease going to another entity after bankruptcy. Amtrak may be opaque, but it's also obstinate when it gets in a fight. See also: its relations with the MTA in NYC. It's basically a railroad.