Spilled oil, exposed wires, and other common sense things should be looked for as well. If you see something you are not happy with, speak up. Good indys will make it right, as they want your repeat business. Some projects–carb tuning, handlebar/foot peg adjustment, etc.–will require follow up work, and most will tune on your bike again two or three times without charge–or until you’re both satisfied. If something does bother you, bring it up immediately or within a couple of days of picking up your bike.
 
Don’t wait until a month later after you have already bad mouthed the mechanic. Good reputations get ruined by selfish bikers who should have spoken up.