A default 2013 site comes with a big block of options in the middle of it. We always recommend removing it, let’s explain why, starting from left to right :

Share Your Site – share what with whom?  It is far to early to start sharing empty sites with people.  You do the content first with permissions in mind, then do the sharing afterwards.

Working on a Deadline – well, maybe.  That will prompt you to create a task list, is that what you need to do as priority number 1?

Add Lists, Libraries and Other Apps – you will need to do that yes, have you planned what you will be adding and why?  The option to add apps is under the Settings menu.

What’s Your Style and Your Site Your Brand – that will change the look and feel.  Also not really the right time to do this.  Add the content first, then do permissions, then do navigation, then apply a new look and feel.  Change the Look is also under the Settings menu.

Keep Email in Context – this is a new one.  It prompts you to create a Site Mailbox.  Again, not really the right time to do this if you aren’t ready.  Do your staff know how it works?  Who will monitor it?

All these things need to be properly planned.  Take the boxes off, they are still available under the Settings menu if you need it later.

And if it’s still irritating you there, you can always go to Manage Site Features and deactivate it.