It really depends on how you're planning on transporting your Phantom. Do you hike or fly a lot? If so, you probably want a backpack. If you're just mainly going to be transporting your Phantom in a car, then a case might be a better fit.
You can find a list of commonly used backpacks and cases here.
It really depends on where you plan to take it. For me since I travel a lot, a backpack is very handy (carry-on only). I also live near the beach, so a case is very handy. I ended up purchasing one of each for that reason.
If I didn't travel much, then I would go with a case because I can keep the propellers on. I am tired of taking them on and off when I have to put the P3 in the backpack.
When I looked at the options, I was leaning towards a backpack as it would be more comfortable to carry. Unfortunately every single one that I looked at (and I looked at A LOT) seemed to be limited on space. I have quick-release prop guards, an iPad Air 2 (full size tablet), sunshade, spare batteries, extra props, toolkit, cables, charger, and the Quick Start guide that I want to have with me. I couldn't find a backpack that looked like it would fit everything and I didn't want to carry a second bag.
For that reason I went with a wheeled hardcase (a Seahorse). It is as modular as I want to make it, and if I need to redesign in the future (for the Phantom 4 for example), all I have to do is buy replacement foam and reconfigure again. I have all the space I need in the case for all my crap, and everything is safely spaced apart in it. It's beefy and definitely not as lightweight as a backpack, but it has a pull handle and wheels so it's easy to move. My 2 cents anyway...