The way the US patent system works compared to other countries is that it's closer to copyright (though not quite copyright): any crappy idea can be patented as long as there's no prior art. The burden of proof is on those who own the patent and those who want to challenge it on court. The Bureau registers everything and then lets the businesses fight in courts.
This approach gives the US an advantage on the international patent market too: an American patent holder has the priority rights in other countries where it wishes to register the same patent.
All this kind of makes sense - kind of - but in practice there seem to be a lot of crappy patents with prior art that remain unchallenged and sometimes even confirmed in courts despite prior art.
This is what's broken. 1-click checkout shouldn't have been registered not because it's crappy but because there were web sites doing something very close or even similar under a different name. Those businesses either never bothered, were too small or went out of business by the time Amazon could be challenged in courts. I believe there are many more examples like this.
Someone has to take the burden of identifying prior art. The PTO doesn't seem to be interested, it's just extra work for them which as a govt. agency they tend to minimize. Businesses that could present prior art can be too small or even out of business by the time a patent is registered.
I believe it's a matter of some additional regulations but because I'm not a lawyer I can't really say how to fix this system.