The reason for this is way too much power for concentrated in these institutions and they started to overstep their authority. For example the EPA tried to implement a cap and trade system even though congress rejected such a system which is a clear sign that the EPA had moved away from just enforcing laws to creating them .
If you are gonna centralize power like this then yes it’s only fair the president gets their way because at least they are elected unlike all these bureaucrats. Of course their are some exceptions but the civil service should not act like it’s own branch of government under any circumstance.