@ryandonsullivan for the love of all things wordpress, please stop using short codes. It wrecks future themes.
— Michael Meulstee (@artisticdork) May 28, 2014
Agreed (mostly)! For inexperienced WordPress users, a theme with a plethora of shortcodes is great. They will let you add all sorts of fancy design features and even add new functionality. I’ve been there. However, most users are likely to change their WordPress theme at some point and if you’re pages and posts are riddled with shortcodes specific to one theme, it will be a major pain in the ass the replace them all. The more content on your site, the more likely you are to miss some. If you only have a few pages and/or posts, then you’re probably fine. I would consider it best practice to use non-theme-specific shortcodes that you know you will continue to use (i.e. Gravity Forms shortcodes). Take the steps now to avoid potential headache tomorrow.
While on the subject of theme-specific shortcodes, you may also want to consider not using theme-specific functions in your functions.php. When you switch themes, you will have to move your functions.php code to the new theme, which increases the risk for errors. Consider placing your functions.php code into its own plugin.
For a more in-depth look at why theme-specific functionality (including shortcodes) is a bad idea, check out Steven Gliebe’s post on avoiding the “theme lock-in effect”.