I've been transitioning over to more of a lean gains diet too, but still eat more than 3 meals per day. Leangains style / paleo substance with more of a dietary focus on nutrient partitioning.
If you eat fewer meals, your calories go up each meal (depending on your goals). If your cals are excessive, they go to waste. Personally I don't like to take in excessive amounts of cals over each meal, I don't want to gain excess fat, so spreading out your cals makes more sense when trying to gain lean mass (or even lose fat). I work in higher cals / carbs around workouts but then still have several smaller meals, and less in the morning, sometimes only BCAAs.