The documentation for the Setter.Value property has the following note:
Windows Presentation Foundation (WPF) and Microsoft Silverlight supported the ability to use a Binding expression to supply the Value for a Setter in a Style. The Windows Runtime doesn't support a Binding usage for Setter.Value (the Binding won't evaluate and the Setter has no effect, you won't get errors, but you won't get the desired result either). When you convert XAML styles from WPF or Silverlight XAML, replace any Binding expression usages with strings or objects that set values, or refactor the values as shared {StaticResource} markup extension values rather than Binding-obtained values.
As a workaround, you could try using a RenderTransform instead:
<Ellipse Stroke="{Binding Color}" Fill="{Binding FillColor}" StrokeThickness="1" Width="40" Height="40">
<Ellipse.RenderTransform>
<TranslateTransform X="{Binding X}" Y="{Binding Y}"/>
</Ellipse.RenderTransform>
</Ellipse>
