That will be solved in part if patents get assigned a value (on which 'damages' etc. are based) that are proportional to the work that went in. For a software product that contains thousands of good ideas, the value of each of those will be only a fraction of the value of the total product.

Then, of, course, the idea of blocking sales of a product because of infringement should also be completely abolished -- some money should be the most you can get.

At the same time, a successful chemical compound might mean tens of billions in sales. A modest software innovation might have a very niche application with much smaller sales.

Is a small research team less entitled to protect their novel work than a big corporation?

If you use the word "entitled", you're thinking about this wrong. Patents are not designed to protect fundamental rights (e.g. to a "reasonable" profit), they are designed to maximize societal good by balancing a monopoly incentive with the benefits of open use.