Well, I could go on for a while about the ball and what would be done in an ideal world, but it seems unlikely anything of substance will change in the equipment, so the architects are the ones who must change to accomodate a different game.
So what can architects do to encourage a greater variety of shots, such as shots that run into the green? They need to resist the urge to raise greens, put bunkers in front of greens (or leave gaps less than 10 yards wide and claiming they are there for the run-up shot) Create contours in front of the green that increase the effective landing area for a well played run up to make it a more attractive option, an easier shot for those players who know how to play it. Such a design also has the side benefit of making the game more enjoyable for short hitters who often cannot hit the ball high enough to land on and hold even soft greens.
Personally, I am so used to playing the usual "select a club, take a normal full swing" shot I am pretty immune to the effect of hazards or obstacles in front of the green. Unless you give me water right in front of the green, or a serious bunker I don't even think about it. I notice them only when I've gone off course off the tee into some trees and have to play a low shot to escape, and have little or no way for a low shot to end up on the green no matter how well it is executed. If the intent was to punish poor tee shots, then do that, instead of relying on the green complex to limit my recovery options as punishment.
Sometimes the villian is the greenskeeper, quite often holes have been obviously designed to allow the runup, but the greenskeeper has mowed only a very narrow lane in the exact center, with deep rough on either side. The runup is unattractive when it requires far greater precision than a lofted shot. Even if the green is tiered and encouraging a runup I'd rather take my chances at gauging the flight distance correctly versus running down a 6 yard wide lane. For low recovery shots it is nearly impossible because you need to not only hit the narrow lane, but do it with an appropriately curving shot. I usually just try the runup through the rough, and hope for the luck required to keep it from getting stuck.