Like BrewBama I find the key is a gentler boil.
I go 60 minutes too, very very gentle. Just a bare simmer, enough to give good circulation, lid on except for a mere crack, until the last 15 minutes. Then the lid comes off and the heat goes up some to keep it circulating well.
But the index of thermal loading is really evaporation I think. The difference I've seen in wort quality between under 60, gentle, and about 6% evaporation, and any process giving 10% or more evaporation, is night and day. And the impact on beer quality and stability tracks also. Advantages in flavor and aroma, foam, all sorts of things.
So boil length isn't the real thing, it's total thermal loading. Think the area under the time/temperature curve on a graph. You do need some time to utilize hops, and you need good circulation to coagulate protein.
I have read that a good "rolling" boil leads to better hop utilization. However, I do not notice a lot of difference with a bit more gentle boil when I am using whole cone hops. The only thing that sometimes concerns me when using pellets (I have switched to them in a lot of cases because of better availability) in a big hop bag is that I want the hops to be constantly moving around in the bag during the boil rather than forming a big tight ball of goo. A bit more aggressive boil gives me piece of mind on that issue as does using a large hop bag. Full disclosure, I do not whirlpool with my brew system. I have a false bottom and extract the wort from the center of the kettle when chilling. i might modify that in the future.
Based on the discussions in this thread and Martin's article, I have reduced my boil times to 60 minutes from originally 90 and add the bittering addition 10 minutes into the boil. The only beers that get boiled for 120 minutes are my Barleywine, my RIS and my Wee Heavy. Gets me finished with the brew day a bit sooner.