We may have a new bottom bracket system that doesn't suck! Here is a short history of the development of bottom brackets and interface types as I see it:
Cottered and 3 piece cranksets. The cranks were steel and had a narrow tread, but the square taper spindle and aluminum cranks were an improvement and took over for a long time.
The square taper spindle is still the best in my opinion and still widely available, thankfully.
Shimano introduces an Octolink spindle. The spindle is a larger diameter and therefore supposedly stiffer. The outside of the bottom bracket is still the same size though, so that means the bearings are smaller and therefore less durable. The Octolink bottom brackets I have used still seem pretty durable.
The move to Octolink forces the competition to come up with something different or use the Shimano standard. The initial answer is an ISIS spindle, with 8 splines like Octolink but differently shaped. The ISIS bottom brackets are uniformly crappy with the exception of the SKF http://www.compasscycle.com/SKFbb.html units. I could never get more than a season of cyclocross racing out of an FSA ISIS bottom bracket. A cyclocross season (around 10 races and some commuting on the cross bike) works out to less than 500 miles. Not very durable! I can get 20,000 miles out of a cheap Shimano square taper bottom bracket. The ISIS cranks also have a tendency to come loose on the spindle.
Because ISIS sucked, the next and current step were mechanisms with outboard bearings and bearing cups. These allow larger bearings so in theory should be more durable but in reality the bearings are side-loaded, do not last long, and the cranks really have a tendency to come loose.
Now there is a new standard available, http://www.bb30standard.com/ , bb30. I'm not counting the proprietary systems like Trek has going on, because those never last for long. They are designed to be, and will be, obsolete in a few years. But that is another discussion! bb30 is a big step in the right direction. Bottom brackets with bearings press fit into the bottom bracket shell have been done before and are probably the best design- Bicycle Quarterly Vol. 6 number 2 has a good article on the subject.
I'm not a fan of change for the sake of change, and with the possible exception of bb30 there have been no improvements over the square tape bottom bracket and absolutely no improvement over the square taper interface. The issue that people bring up is stiffness. As long as the spindle is steel, it is not an issue. If it were an issue, why is the square taper still the track standard? If anyone would have a problem with power loss from flex in the crank or bottom bracket, it would be a track sprinter. The other issue is weight. It is true that outboard bearing systems due save a small amount of weight compared to cartridge bottom brackets. A small amount. A properly designed press fit bearing system like bb30 is the lightest system.