The major drawback in stopovers is that it complicates planning. A transit visa won't work. A tourist visa requires advance bookings which means more planning. Only business visas give you freedom to improvise. Another complication is the ticket.
Most tourists have a single ticket for their entire journey.
I didn't, and despite dire warnings from ticket vendors, I had no problem buying point to point tickets on the spot. Just because you have a ticket from Moscow to Valdivostok doesn't mean you have to do the entire trip in one sitting. You should be able to step off the train, get another reservation, and continue your journey on another train. However, you will discover that outside of the Kremlin walls, rules can be a matter of opinion as much as anything. Before you leap off the train in a pituresque Siberian villiage, ask someone about the current practice and nature of your ticket.