ISIS are stiffer, and are suppose to be better because they have the grooved shape. But they are more expensive.
Although I've always just used square taper BBs', mainly because it was cheaper.
But over the years I've found they are just as good in the long run, especially if you get a decent one with good bearings.
I've had my Shimano UN53 for about 5 years now....no problems at all.
Hope this helps.