Not sure that this is the greatest advise but i can tell you some of the problems you might encounter with checking a backpack at the airport.
First the ticket agent is supposed to ask you questions about dangerous goods like matches/lighters/any kind of fuel or propellant, even aresols like bug spray, if you have any of this you have to get rid of it or they wont check your bag.
Next you might want to be prepaired for a charge of some kind, most airlines are nickel and diming everyone now even for thier first bag. Generally anything over 50 pounds will get charged more for heavy luggage.
As far as plastic bags go, well you have to consider the bag tag. It gets scanned so they can track it and its hard to scan it with the plastic wrapped around it, so what usually will happen is the we (I'm a baggage handler myself) will rip open the plastic where the tag is so we can scan it. Most of the time its because we have too much to get done and we simply dont have the time to try scanning it several different ways to get a good read on the bar code.
Also it was mentioned earlier that any kind of straps, bindings, buckles and stuff like that can get caught in the belts and conveyers that your bag is going to be riding on. Best to tape them up. I've seen a lot of luggage that has been ripped wide open and all your stuff goes spilling out. If this happens (due to the time thing) we'll find a big plastic tub to put your stuff in a pile and send it that way.
Another thing you may consider is liquids. Any kind of water or drinks you bring are likely going to be frozen solid when you reach your crusing altitude. Your containers could crack and then leak once it thaws.
Also keep in mind that those TSA (Thousands Standing Around) can open your bag up to search it. If you put any kind of lock on it they will cut it off and leave you a note inside with your cut lock.
As for protecting your gear inside, a good rule of thumb i would go by is that if you can stand on it w/o breaking anytrhing your probably ok
Its a lot to remember but most of the time backpacks make it intact with all your stuff