Patents are not supposed to be worthless against larger companies who can just replicate your work without your help.
If people can replicate your work without having to look at any specific about your work, why should your work be patentable?
What about if you reverse the actors in your example? Should large companies with vast warchests filled with patents be allowed to strong arm smaller competitors who likely don't have nearly as many patents with which to defend themselves?
Patents aren't about protecting an idea because the person who came up with it was uniquely qualified to create that particular thing. Any number of people could create the same thing independently. But only one person can be the first person to create a thing.
Patents reward those who come first, those who push a boundary, who create something novel. Novel doesn't say anything about how many hours it took to come up with the idea.
Remember, this patent is from 1996, and soon to be expired. 16 years later the algorithm powering AdWords can't live without it. I'd say this patent was 'ahead of the curve' when it was written.
Injunctions are becoming more rare, and if the penalty is apportioned correctly it would always make very little sense for a much larger company to sue a smaller one, because even a win would cost more than it was worth.
Even with recent changes, the law could due with some strengthening to protect against harassment suits. From large companies against small, and from trolls against anyone. Reasonable costs for the defendant could be carried by the plaintiff in some cases.
If people can replicate your work without having to look at any specific about your work, why should your work be patentable?
What about if you reverse the actors in your example? Should large companies with vast warchests filled with patents be allowed to strong arm smaller competitors who likely don't have nearly as many patents with which to defend themselves?