In a nutshell, putting any extra UI functionality into an ArcGIS tool is an antipattern, as the tools are designed to be portable within ArcGIS and usable from stand-alone Python.
If you have a workflow which necessitates user input, this is a natural place to break the workflow up into multiple tools. Before the input step, write your data and use that data as the input for the next tool, (Deciding to move forward is essentially the Yes/No dialog in your case). This increases modularity of your tools and ensures that they can be accessed arbitrarily from any view - ArcGIS Desktop, Server or from a Python command line. Right now you'll get errors if you try to run outside of desktop and your tool is not portable between 10.x and Pro.
Breaking it up like that also has the added benefit of future-proofing the workflow - say somewhere down the line someone invents a process which removes the need for user input, you can simply string your modularized workflow together in a 'wrapper' style tool, rather than recoding the entire thing.
Hope that helps move things along!
Clinton