My first guitar teacher always tried to convince me volume was the difference, because we somehow had the help of gravity on the way down. I changed guitar teachers shortly thereafter.
In my opinion, the differences are almost always purely tonal quality due to the higher strings being set in motion first. I have very little knowledge of acoustics, but I suspect the sympathetic vibrations of the other strings before you hit them also have something to do with the resulting tone. As a result the upstrokes will have a somewhat lighter feel than the downstrokes. HOWEVER: I believe that it depends on what style you're playing in, how fast you're strumming, how many upstrokes there are where there "should" be downstrokes, etc. I think that a good guitar player, can, in many styles, use his/her choice of strum and still make it sound as desired. Depends on a million different musical aspects of course; hard rock would be more difficult to work it. Light strumming on an acoustic guitar in a quick folk-style song would be easier.
This is my experience as a musician and music educator, not as a professional guitarist, so your mileage may vary. I'd say a general rule would be to use whatever combination results in the sound required without being too difficult or detracting from other elements. If playing all downstrokes even slightly changes the regularity of the pattern, then (in my opinion) you should alternate and focus on getting an even-ness of sound.