It depends on you and your time.|
If you have time ( and money! ) it is better to make at least one stop on the Moscow-Irkutsk route.
Never believe anybody that Ekaterinburg is 'better' than Krasnoyarsk, etc. They are all more or less alike- Zarist, Soviet, New Russian. Also in terms of nature they are all similiar: some hills in Perm, Ekaterinburg and Krasnojarsk.
You have plains in Omsk and Novosibirsk. It is rather making a stop somewhere for a wash and some stabilization from sometimes smelly and shaky trains.
Stationed in Omsk of course we want to propose you a stop-over in this interesting city and visit its outskirts.
Another interesting thing about Omsk is its proximity to Astana- new capital of Kasachatan. Here is what one backpacker wrote about this:
Impressions of Astana