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What if a startup spends ~2 years coming up with an idea, launches it, and gets noticed by a Big Company before the site gets big. What's to stop the Big Company from just implementing the idea themselves in a slightly different form? Would the Big Company still buy the startup/how will the startup be compensated for its work?

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I'm not sure that's much different than the state of things today. The status quo version of your scenario is that startup has an idea, patents it, spends 2 years implementing it then launches. Today, even before startup launches, Big Company can see the patent, build a similar system that's just different enough to not violate the patent.

Today, Startup can sue, alleging patent violation, but most startups don't have the cash on hand for an extended patent battle anyways.

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