The iPad 3 does take a lot longer to charge--it has a 70% bigger battery than the iPad 2, but the charger is still only a 10w charger as before.
In one of my tests, charge from 0% to 100% took 7 hours, 30 minutes, and 47 seconds, or about 4-5 minutes per %. Also, the last few percent of the battery are always the longest to charge because it slows to a trickle to prevent damage to the battery. So you'll probably see it take an hour or more to get from 90% to 100%, whereas from 10% to 20% only takes about 40-45 minutes.
Lithium batteries wear out faster with deeper cycles (i.e. fully draining, fully charging). So, whenever possible, it's best to keep it topped off rather than wait for it to fully drain before the next time you charge it.