If I'm not mistake, shapeshift charges .5% fee on all shifts. This is compared to .15%-.25% on most exchanges. If convenience is worth more to you, shapeshift is the way to go.
I tried shifting BTC to LTC yesterday, and even though the transaction to deposit my BTC to ShapeShift address was confirmed on the blockchain, ShapeShift order is still stuck in "Awaitting Deposit", almost 8 hours later. I now have to deal with a support ticket for a refund. So, I'm not even sure that convenience is something you get with ShapeShift, all the time.
I have to admit, it was convenient when I used it previously, but it seems it's not always working the way it is advertised.