A lot of what you are saying has already been considered.
The auto brake does not bring the nose down with a thump; it is easily controllable. Having the brakes come on early, as soon as touchdown occurs, is a good thing under all conditions. Once the airplane is slowing the pilot can take over manually just by pressing the brake pedals, if that is what he wants to do. Point is it should always be armed for landing, wet or dry. Boeing philosophy. Idiot proof, it was thought, but apparently not completely so, especially when airlines think they know better.
Spoilers are essential, which is why they are automatic and if forgotten, will automatically deploy when the reverse is selected.
The problem with late reverse is due to improper operation, not design. We have all done it at some time, but usually learn how to do it right early on. Hopefully during the initial simulator periods, and not on the airplane. If the reverse is pulled with the throttle(s) not fully closed, the linkages lock up and it takes some force to push them back down, properly close the throttles, and try again. Takes time, during which the residual forward thrust, if above idle, will retard deceleration, or at best will not help to bring the airplane to a stop. Some airlines even mandate that the reverse should not be pulled until the nosewheel is on the runway, contrary to Boeing procedures, and another of the many examples of idiocy in airline management.
All accidents can be traced to management; poor policy, training, supervision, support or whatever. In this case, it is apparent that a lack of understanding of Boeing procedures, and adoption of their own variations thereof (how many other deviations from standard do they have, in addition to this one? Most (all?) airlines have this insane idea that they know better than Boeing how to operate the airplanes, never mind that Boeing is staffed by experienced people and have the advantage of knowing what works in ALL fleets, not just the tiny sample the particular airline has to work with) led directly to this accident.
Root cause. Fix it and prevent similar accidents forever.