After society stage we'll obviously have different parties, and one of these will gain political power.
Then, if this party (the one you "control") loses influence and another party gains power... what about strategy mode? You can't control a nation that isn't under your influence.

So, we can choose to ignore this and let the player control his nation anyway, or we can do this:

When your party loses power, you can't use strategy mode, or you can use it only partially.
Then the player should "use" org mode to control the party leader and try this way to get influence again.

What else?

Let's discuss here

In strategy mode I thought you just assisted whatever party is in power as a sort of limited-god-like thing... So you aren't actually any specific party.
Some-one else will be able to explain this better.

The real problem here isn't of parties, it's of a revolution or something. We shouldn't let the player control their government if it's been taken over by another force. They should have to regroup and rebuild, and either
-leave and create a new faction
-get high into the current government that replaced theirs
-try to take over the nation again

No, 2 is good in scio's post. The amount of historical examples that come to mind is astounding. For example, Queen Victoria supported both the Whigs and the ... tories? Anyhow, whichever party it was politic to support - as in, whoever was in power and would support her in return.
In addition, we have governments like that of Argentina - not picking on argentinians at all - that at some points in history have had revolutions as stand-ins for elections. And while high-ranking political figures, like Juan Peron, have had to go into exile when they've fallen from power, people with less-politicized positions can hang on through many transfers of power, whether violent or no. The truth is, we need them to keep things running.

We're a little further removed than that in strat, and org lets you choose whom you are.

What if your government type does not include parties?

also if someone else takes control of ur government u can throw a rebellion that would be nice to see

Has anyone read up on the Nation Editor? When you give more of the power slider to the people, sometimes they change things that you don't want changed, and in turn they are happier. Alternatively, if you're talking about elections, that will just change the likeliness of certain leader traits popping up.