Pro: Arc Hydro Tools should be listed in logical order: Bring back the toolbar!
In Arc Map, the order of the Arc Hydro tools, for very good reason, follows the order in which you must execute the tools. For example, you can't (shouldn't) run flow direction until you fill sinks, and you get some really wonky results trying to run flow accumulation on the sink raster without first running flow direction.
However, in Pro, all you get is a GP Toolbox, with the tools listed in alphabetical order, not order in which they must be run. FWIW, the Arc Map toolbox does the same thing. Not an issue though, as in Arc, a handy toolbar presents the tools in the correct order. Not an issue for an experienced hydrologist, but a great leap of "this is now harder to do in Pro" for folks learning how to use Arc Hydro. "Make a custom toolbox and add it to the analysis Gallery" someone will say.
Harder. More time. Arc Makes it easy, why can't Pro?