When I taught in a PS we did lower first.... Now that I am homeschooling ( our first year)......I teach both at the same time, My son has a processing delay but did really well learning both.
I teach both, I use the letter of the week style, we actually go through the alphabet twice. The first time through, i introduce both upper and lower for recognition, however, we work on upper case print. We also stick with one letter sound for each the first time through, and the second time through we introduce the soft sounds and the short sounds. After doing it this way, they seem ready for the first grade phonics program I have.
((edit: sorry, I wrote that we work on the short sounds the second time through, I meant that we work on the LONG sounds the second time through. Short sounds are introduced first time.)) It's just how I'm used to teaching it now that I'm through three preschoolers and have only one left.