Well, I can see a few options...
"The Stalins View Option": Triggering "the Great Purge" will give you MASSIVE short term penalties(loss of officers, loss of experience, etc.), but in return, will also give you a HUGE influx of political power, which you will NEED if you plan on enacting the five-year plan(s), reforming the army into a professional rather than conscription-based force, and other big long-term projects that were IRL responsible for turning the USSR into a cold war era super power.
This approach has the benefit of turning the Great Purge into an interesting choice: Ignoring it is safer, and should help you hold off the Germans more effectively in a "standard" WWII scenario, with the Great Purge serving as a risky(and entirely optional) long-term venture.
Could also be implemented quite easily into the current NF-system, by simply making the appropriate focuses REQUIRE you to first activate the purge.
"The Dictator as Obstactle Option": Dictators are unpredictable little bastards, who may decide to throw events both major and minor in your face with little to no warning - such as the great purge - and it's up to you to make the most of the situations you are given.
The advantage of this approach is that it adds variety and makes the game just a little bit less predictable; you may know your dictator of choice is going to screw you over, but you don't know when or how. Especially fluffy for a German player since, if I've understood it correctly, this is basically how the relationship between the German High Command and their "beloved" Fuhrer worked.
Somewhat less fluffy for the soviets, perhaps, but it should still work out quite well as a gameplay mechanic
...kinda doubt there's still time to implement these things before release, though... perhaps in a DLC..?
EDIT: oh, we've moved on to Trotsky... really need to learn to type faster... erm... well, he makes for an interesting option, but I don't think it makes much sense for him to automatically unseat Stalin unless countered - would probably be better as a national focus of its own; "Unseat Stalin", massively improves your diplomatic abilities, at the cost of NU, political power, and possibly industrial efficiency...?