Gah, Russia should not have THAT many problems to industrialise, I think. I disagree with the idea that Russia's size hindered industrialisation, since most of Russia was in the west anyway, both in terms of population and technology. There were two real problems for industrialisation.
Serfdom, as you said, was a big problem, but it was solved pretty neatly; the unrest was limited and controlled, and redemption payments made the nobility happy. I think this should be a feature to be considered in the game; the possibility of emancipating the serfs, and the extent at which to do this - all of this directly affecting your stability, of course.
The second problem was the nature of the Tsars; they were all too conservatory. Even Nicholas I, despite all the "Tsar reformer" crap, was a conservatory who believed in all the values about authority and tsarism (in fact, he only emancipated the serfs when forced by the Crimean War). And Alexander III and Nicholas II were both educated by the reactionary Pobedonostsev, so they didn't get much fresh ideas. This must be added to the fact that their government was chaotic and inefficient.
But except for serfdom - which as I said, should be given the option to solve to the player - it was a problem of crappy leadership of the country, not of particular social conditions. After all, look at what Sergei Witte did at the end of the 19th Century: Russia's industry made huge leaps forwards. Without World War I, it was presumable that Russia could have become an industrial power comparable to Germany before 1940. I am convinced that this could have happened much earlier, if only someone had gotten to work on it.
So conclusions? If Russia is to be given a handicap in industrialisation, this must be limited to the nature of the leaders and the chaos in the government. But it should only be limited to that, and not extend itself to unalterable social conditions.
Oh, and I think that a great emphasis should be given to the international effects of economy. After all, Russia industrialised through foreign investment, so it should be possible to ask huge loans, and have nets of credit and debt here and there creating an interesting and complicated world balance - which would, of course, affect strongly the diplomatic behavior of the AI, giving new motivations for waging or not waging war.