For sure, touring such a distant, yet exciting route is always full of wow-moments and totally depends on your time, budget and a little bit of imagination. As we have already mentioned, the term Trans-Siberian may include also Trans-Mongolian and Trans-Manchurian extensions so again, it's all up to you.
Of course, traveling directly from Moscow to Vladivostok and seeing all the passing beauty just from the window of the train is an unforgivable mistake considering all the possibilities the Trans-Siberian route offers. If you plan many stops on your way, be sure that you manage all the logistics carefully as in such case you'll need to book lots of trains. Anyway, you may always choose an easy way and turn for help to us, which is going to be more efficient and worry-free.