To the OP - like you, I'm using BrewMate to scale back many of the BCS recipes from 6 to 3 gallons. I haven't had any problems going this route at all. I've brewed 8 batches that way and they've been awesome so far.
I think the problem lies with either your personal expectations of the style, or something within the brewing process. If your beer is too thin and lacking character, I'd take a close look at your mash temps. Consider mashing a bit higher to increase body and decrease wort fermentability. It could also be a yeast factor. You might consider a different strain that will increase body and amp up the malt character (WY1450 comes to mind).
Also, keep an eye on pitching rate with the 3-gallon batches. I think overpitching can increase attenuation a bit (although that's strictly a gut feeling at this point - I have no data to support it).