Check the Campaign rules (top of this forum) for the difference in Choosing an Earth force allied with Sheridan or Clark. The choice really only matters near the end of the campaign, when you've got 2+ control points.
You can then opt to field Sheridan if you allied with him, or the mighty Shadow Omega class ship if you allied with Clark. Its really just a matter of personal fluff preference and if you've always wanted to try out a Shadow Omega model.