I used to go short AM, long PM until I had a class conflict that reversed that order. The results were the same in that I improved the seasons with short, long and improved going long, short.
Right now, a few years out of college, I have time and work constraints that make it so that I have to go long, short and it's working out just fine.
The one thing I liked better about short, long was that on structured workout days, you start your warmup in the afternoon already feeling a little warmed up in the legs, and you really feel ready to rock for your workout by the end of the warmup.
The bad thing about short/long for me was my stomach/bowels. I am a first thing in the morning pooper so if I get up early I can poop a bunch and not have to on my run. If I have to go longer in the afternoon, the chances of having to poop sneak up and I find myself hiding in bushes rather quickly, losing either my socks or the sleeves of my t-shirt.
Also going long, short helps me consume more calories over the day because my stomach really seems to be ready to have food settle after a longer run. And I don't have to make sure my stomach is as empty for a 4 mile run as for a 10-12. So in general caloric consumption goes up from going long/short, which I need.
The problem though for going long/short is being warmed up enough for a workout early in the morning, so I usually just add on about 1/3rd of the warmup. Aka I go 4-5 miles.
I don't know if you have stomach issues etc, but that is my take on the whole thing.