jeez its not rocket science just take the time to pick the shot out before you cook it...........
ive found a tooth pick and slim needle nose pliers to be very helpful in taking shot pellet out of a squirrel or rabbit. or something you can do to minimize the amout of pellet in your game is use larger shot pellet, larger pellets means less pellets and the chances of the pellets making a complete pass through it much greater. for squirrel since they are pretty tough critters and need some pellet penetration to kill them I use number 4 or 5 shot and most of the pellets pass all the way through. Rabbits on the other hand dont take much to kill, Ill use 4 or 5's if they are skittish and my shots are fairly long but if they hold and I can get close shots then Ill use number 8 or 9 shot, with that small of a pellet they tend to not go deeper then the skin and are usually sitting on top of the flesh and most of them fall out when skinning the rabbit you might have to pick out a few. good luck