What is the time/mileage on the 12 speed hydraulic brakes system? They are more progressive when simply standing in your living room pulling the lever. In a perfect system it's not hard to make the lever nearly touch the bar. In outside in motion use however, the equivalent lever position would be beyond panic stop wheel lockup even if it isn't readily appearant while standing next to the repair stand. In other words it isn't fair, accurate, or helpful to compare rim to hydro lever feel. There is no useful comparison other than performance in use.

You likely have heard about pad/rotor bed in. In a ride or 2 hydro gets really good. Don't be too quick to judge. The pads need to advance to the rotor the first couple of uses. Then they need to mate with all the surface irregularities, if any.

Of course, if the hydro lever stroke (travel) change is a new phenomenon then something may be up. New pads, centered calipers on rotors better than minimum thickness and a system bleed is a good place to start. No leakage anywhere?