Independence Air use to fly as Atlantic Coast Airlines. They were a regional carrier that supported United Airlines on the East coast. They have been around for quite a while and their pilot training matches pretty closely with the Major Carriers (UA, AA, DL). The only real difference is the size of the jets. While they are smaller, they have all the advanced eletronics of the larger planes (737, 757, Airbus etc). The regional jets are very new and reliable planes. They Cruise at the same altitudes and speed as the big jets.
As fars a bumps/shakes, with it being a smaller plane, it is a little more noticeable, but not that bad. Pilots will do everything they can to avoid those bumps to make the trip smooth.
When UA went into bankruptcy, they asked Atlantic to continue flying for them but at a cheaper rate. Independence was looking to keep the same or get more so they decided to jump ship and create a new low cost carrier like Airtran, Southwest, Jet Blue. The industry was watching and what happened is not what Independence had planned on. They have struggled trying to gather market share and passengers and have bit hit really hard by the sky rocketing fuel prices. They have been teettering on bankruptcy themselves but have avoided it thus far.