All my AG batches are 3-gallon; it's a great batch size. I also do 5-gallon extract batches. I generally use my 5-gallon carboys as primaries for my 3-gallon batches. Works great.
I also use BeerSmith to scale 5g recipes to 3. But you do get some inconvenient numbers. So I usually round the numbers manually. Maybe move the time of additions to keep the IBUs.
Mechanically, beer recipes do scale. The one thing that stays pretty constant is the boil-off rate of a given system.
One piece of advice. Don't get wrapped around the axle about precisely scaling recipes. There is art and science in brewing, embrace the art too.