The only reason the thalmor haven't invaded is because of the empire. They still have power and a large enough army to give the thalmor a run for their money. The war was huge and it was basically a 50/50 chance but when the thalmor were about to win the empire signed the treaty as a last resort. They gave up talos but are dealing with the thalmor and not allowing them to kill all of man things are peaceful for the time. If the stormcloaks are independent then short term results would show a new nation of man that had no influence from the thalmor, but long term Cyrodiil would lose its power and be consumed by the thalmor and so would hammerfell and high rock. Skyrim would surely fall and the thalmor would win. If the Empire keeps its provinces and starts to build power again they will continue to deal with the thalmor and keep peace until the thalmor weaken (which they will because they are are a radical controlling government and revolutions will start to occur, and then the thalmor will be too focused on what the empire is doing that they won't pay enough attention to their own land) and the Empire will soon be able to either take over valenwood and SI or make an alliance with whatever new government forms.
So we can go with the short term solution - the stormcloaks
or we can go with a long term solution that will keep the thalmor at bay and make sure no one gets destroyed until the thalmor fall on their own or they can be conquered - the Imperials.
Ok, we agree: Thalmor = bad. That's a good place to start.
But let's talk about how the Altmer wage war. There's a thread on this in the lore section of this forum here: http://www.gamesas.com/index.php?/topic/1253125-altmers-ability-to-wage-war/
In your argument, you're making an assumption that I think you should stop making. Don't get me wrong, it's a very reasonable assumption, and I think many other people are making the same assumption.
You're assuming that what the Thalmor WANTED to do was immediately kill everyone in the Empire, and that the Empire made them stop it by signing the peace treaty (the White Gold Concordat that outlaws the worship of Talos and allows for Thalmori agents to infiltrate the Empire and root out the cult of Talos.)
But let's question that assumption, as reasonable as it seems to be. After all, by all accounts, the High Elves have longed to get rid of mankind. Why wouldn't they simply try to destroy them outright as quickly as possible? Well, that's how you and I would do it, but that's not necessarily how the High Elves would choose to do it.
Let me draw you an anology. Suppose there was something you wanted really, really bad - Skyrim, for example. Well, suppose I said that you could have Skyrim, that I would give it to you, but not for 100 years. That'd be kind of stupid right? We'd both be dead.
Now pretend you're an Altmer that lives to be 1,000 years old. Waiting 100 years doesn't seem so bad anymore. Still a long time, but not as bad as it would be for us. But instead of wanting Skyrim, they want the destruction of humanity. They've already been waiting for 1,000's of years. Eras, aeons. They are a very patient people.
Might they have a reason for waiting? YES! Quite simply, they'll bleed the Empire dry slowly, bleed humanity slowly, watching us bleed to death over a period of decades, growing weaker and weaker with every passing year. Eventually, those of us who remember the Great War will die off, and our children will never know a world without Thalmori agents permeating their lives. In a generation or two, they will have wiped out Talos worship altogether, blotted out his memory from the hearts of man, and somehow that weakens humanity even further.
Then humanity will be ripe for the taking. Then the war will be much easier, fraught with much less risk, much safer for them. They can watch generations of men come and go - but they remain, patiently plotting our doom.
Time is on their side. Their goal was the Concordat. They WON. They achieved their objective. They probably could have slaughtered all of humanity, but that would have cost many lives and lots of money. They are cowards, content to bleed us slowly for centuries if they have to before they finally strike.
While you and other loyalists wax poetic about the strong noble Empire that stood up to the Elves and only made concessions as a last resort, all the Elves are wringing their hands because in their minds, the destruction of humanity has become as immanent as our getting Skyrim in 2 days. RIght now, Elves are in their chat forums talking about what they will do when they become gods again.
There is no hope in the Empire any longer. Its fall is certain. Its doom already written. There's no coming back from this. It's only a matter of time. And time is NOT on our side.