How would startups suffer? The stated purpose of the H1B visa is to fill in for labour shortages. If there is a labour shortage you would expect costs (salaries) to rise. Basing the visas on salary should help to identify and target areas where labour shortages actually exist. Bringing more workers in should make all workers in the field cheaper than they would be if you didn't bring in the extra workers. This should benefit startups even if they don't hire H1Bs.
Also, the current system isn't great for startups. There are far more H1B applicants than there are visas. There are a few large companies that bring in the majority of H1Bs. These large companies can afford to apply for thousands of H1Bs knowing that only 50% or less will be approved. A startup hiring a handful of people can't afford to put in the application for a handful of people knowing that there is a very real chance that none of them will be approved. Even if they are approved, applications need to be in several months before the visa is issued. How many startups are hiring in March for a position they won't need to fill until October?
Also, the current system isn't great for startups. There are far more H1B applicants than there are visas. There are a few large companies that bring in the majority of H1Bs. These large companies can afford to apply for thousands of H1Bs knowing that only 50% or less will be approved. A startup hiring a handful of people can't afford to put in the application for a handful of people knowing that there is a very real chance that none of them will be approved. Even if they are approved, applications need to be in several months before the visa is issued. How many startups are hiring in March for a position they won't need to fill until October?