I run all mediums as most know by now ..
Upper entrances as well, it seems to cut down on the travel stain quite a bit.. I have also noticed (Imagined?) with upper entrances the super frames are drawn out a little faster.
I try to run an unlimited brood nest most of the time. using all mediums means i am not stuck with medium frames filled with brood that I have no place to put them because the lower boxes are deeps.
I have had queens FILL the center 6 frames of 4 mediums with brood. If those queens had been restricted they would have swarmed. The bonus, was STRONG hives that made honey stacked seven and eight boxes per hive.
For those with a few hives it wont be as important, but to me, being able to pull frames from wherever I can to make up a nuc is a HUGE bonus.
I can still lift a deep of honey, provided I havent hurt my back recently.. AND, provided i dont hurt it WHEN I lift that deep of honey.. A deep of brood, pollen and honey is heavy enough.. i still have two or three deeps in the mix... i have NO problem what so ever cutting them down. The biggest down side to doing that is losing all those drawn frames. it is pretty easy to go from deeps to Mediums slowly, by rotating out one of the bottom deeps each year, and put a medium back on top. Cut the deep down, repaint it and its ready to be used.
I think if you WANT to use deeps, then you should! i also think if you are going to use deeps because thats what "everyone" does, then you need to rethink beekeeping. You need to keep bees how YOU want to keep bees, not how someone says you HAVE to keep bees. Yes, there are some things bees NEED.. I think Randy Oliver puts it best;
"There are no “shoulds” in beekeeping other than practicing good animal husbandry. Bees only need a dry cavity, food (nectar, pollen, or syrup and pollen supplement if lacking from natural sources), and parasite management. My basic rule is to not do anything unless you completely understand the reason that you are doing it!" -- Randy Oliver
Beyond those basic things, just about EVERYTHING is variable.. That is why it can be so confusing starting out.