1. Using more muscles does not mean you burn more calories. If a team swimmer is smart they are going to use as good of technique as possible to minimize effort needed by their muscles, and use the benefits of the bouyancy to their advantage.
2. You seem to think all the muscles funciton separately. When you run AND swim all your muscles are being used. Muscles do not funciton separately, rather as an entire network that allows one muscle to do one task which allows the other muscle to do another task.
I was on swimteam for two years, and I\'m also a cross country runner. Swimming was a good workout but running has more factors that make the body exert more energy. More oxygen is burned due to the body moving faster, thus meaning more calories are burned as more liters of oxygen are used.
Running outdoors presents weather: cold weather makes your body have to burn MORE energy. Not to mention gravity, uneven ground, hills, mud, and also extream heat. A pool allows a swimmer to have a more stable enviorment for their body to be working out in, and thus their heart rate is lower as less adjustments are needed.
Mainly though, it really depends on how hard you are working... but my roomates say they burn 1,000 calories swimming in an hour, and that\'s total bs. Mainly because they don\'t swim for that long in one period. A runner can run straight for an hour and burn around 800 calories going at a medium to heavy pace.
As far as difficulty goes, I think swimming is easier once the technique is learned, because the technique allows a swimmer to use as less energy as possible to get as fast as possible. Running has important technique as well, but pure cardiovascular and heart strength is more vital in this situation just to keep the legs moving fast enough because of gravity. Running has more factors working against the person, than swimming.