I apologize for my extremely limited ability to aid you in this particular playset trajectory; but to understand better and help you to sound out these problems: who're you playing as?

Addendum; I would think that for you to make the Federation main shipyard complex at Utopia Planitia; you'd have to do significant research before you could; usually it takes many decades of game-time research to be able to build such a specialization of one of your planets to be able to build that particular ship factory base.
Don't try to build it when you start the game; take your time, a long time before you begin to build that particular ship factory base.

The Xindi only are created after the probe event. Utopia Plantitia requires research as jamcarmody said.

I had merely guessed that like any fortress world, and the Star Trek novels, that Utopia Planitia needs specific research to be able to be built, and it can take quite a while to be able to do that, let me tell you!
Though, you want a good place for a fortress world? Try Zakdorn; that'll have a *LOT* of troop production, especially if the Zakdorn have built their military academy prior to absorbing them!