With your suggestion only the largest companies would be able to apply for patents. For Apple, Google or MS a couple of million dollars means nothing for a patent. But it infeasible for a startup or smaller research groups.
Instead, only the largest companies can defend patents, which is just as bad, or worse.
Patent application fees should reflect the real cost of processing the application. If improving patent quality requires an increased processing cost, then this should happen, since not doing so unreasonably increases future litigation costs for everyone. Subsidizing small companies' applications might then be reasonable if we want to promote startups and smaller research groups, but there's no reason to subsidize the largest companies' applications.
This is already the case. While with low fees you can get a patent issued as a smaller institution, in practice only institutions with in-house legal teams can afford to defend them. Those include, unsurprisingly, patent trolls and megacorps. The cost of patent litigation is in the millions regardless which side you're on.
