I think this would be better stated as “funding” — it's not like nobody at Amtrak has failed to think about the hotspots for them, it's just that they are in the unfortunate position of being expected to service a lot of [now] marginal routes against both very well funded alternatives, but they have limited governmental support for the kind of major infrastructure changes they need to dramatically improve their offerings.

A completely private business could, for example, simply discontinue unprofitable lines or acquire long-term debt to fund a major capital investment but they were created specifically to avoid closing routes and debt is a political hot potato. A government service could point to greater societal benefits to justify funding out of general tax revenue but Amtrak is expected make enough in ticket revenue that they're perennially short of cash. A large part of the problem is simply that railroads have high base costs which can be made up in volume but their service costs more than alternatives because we don't subsidize rail anywhere near as much as highways (for example, DC to NY on train costs more than a bus, but I-95 isn't a toll road funded only by users).

Edit: just to be clear, I'm sure that they're just as flawed as any other group of humans — it's just that whenever you see some obvious problem holding an organization back, it's almost never the case that nobody there has thought about it.