I have yet to see an advantage to the eticket system - except to Apple who sold Amtrak a whole lot of new iPhones - good marketing. As demonstrated by this thread, it is still causing problems and misunderstandings months after implementation. My recent trip was fine going with one of each.
There are considerable advantages to the eTickets, not the least of which is that one doesn't need to first obtain a traditional paper ticket. This helps people boarding at stations that have no ticketing facilities. Next, Amtrak gets real time manifests now, something that the NTSB & the FRA have wanted for years. It improves Amtrak's revenue control. And there are other advantages I'm sure.
Some of the problems are of Amtrak's own making. For example, this idea of cancelling entire reservations for people who no-show. I understand why Amtrak wants that function, so that they can resell space down the line of no shows. The problem is in the implementation, in that Amtrak can't seem to depend on conductors missing checking people in.