And what does the Empire have to show for it? All their forts in Skyrim remain abandoned, there's hardly a legion presence to speak of and they're forced to recruit locally in order to quell a rather dangerous insurrection. What's keeping the Empire? Where are the armies they've been training? Is this just a product of Skyrim's presentation/gameplay/scaling?
My sense of the metaplot is that the Empire was at its strongest during the reign of Tiber Septim. It has had its ups and downs, but generally gradually declined through the Third Era. Uriel Septim VII was the most effective emperor in generations, but was also faced with some of the greatest challenges -- reconstructing the Numidium solved many problems, and it's noticeable that the one province we haven't heard any bad news about has been High Rock -- but the Empire was clearly nearing the point of collapse after centuries of weakening. Martin Septim managed, against all odds, to end the Oblivion crisis and allow the Empire a little more time. The Medes have just been watching over the largest of the broken pieces; they lack the mythic resonances that the Septims held.
The civil war in Skyrim is near the endgame. Without Skyrim, traditionally the most loyal province after Cyrodiil, the Empire will be too weak to survive. Without Talos, the Empire will be too weak to survive. You can't really choose one over the other. Either path, taken without consideration of the significance of the Dragonborn, would mean the collapse of the Empire, the success of the Thalmor, the liquidation of the structures that reinforce the Mundus, the extinction of humans, and the dissolution of Mundus.
However, it is not a coincidence that the Dragonborn appears just at this moment.