The issue for startups happen when you take a permanent residency application into account. For instance, I had a friend who got into two great startups who were willing to sponsor H1-Bs. He really wanted to work at either. However, he also wanted to apply for his permanent residency within 2 years to continue staying in the US. However, a company needs to have certain revenue (besides other minimium requirements) to be able to apply for a green card. Both the companies checked with their lawyers and they did say that it was a big risk factor when it came to applying for a permanent residency. So he actually ended up passing both offers.
In retrospect he would have been fine since both companies ended up getting acquired by Intel and Google, where he would have been fine. But that is part of the risk involved.