I have filed one bug in VS2013 feedback forum for this issue. It can be tracked here: https://connect.microsoft.com/VisualStudio/feedback/details/898599/
Based on suggestions from AdrianHHH, I am currently doing this to get all the children of a control. This returns all controls including HTML5 controls as HtmlCustom.
private List<UITestControl> GetAllChildren(UITestControl uiTestControl)
{
var child = new HtmlControl(uiTestControl);
child.SearchProperties.Add("InnerText", "", PropertyExpressionOperator.Contains);
var items = child.FindMatchingControls().ToList();
var trueChildren = items.Where(i => i.GetParent().Equals(uiTestControl)).ToList();
return trueChildren;
}