Without the Empire, even in it's weakened state, it's unlikely Skyrim would be able to oppose the Dominion.
Without Skyrim the Empire loses a province and the resources from it and becomes much more fragile, too tempting a target probably.
Neither side truly wins in this war.
The Aldmeri Dominion is the one who really benefits.
which would suggest that they are not confident enough to take skyrim if it was isolated.
The Dominion effectively won the great war. Skyrim forces would have been involved (being a province of the Empire), and yet even then the Empire lost. Skyrim alone would have less resources and fewer allies to call upon.