While at Microsoft, Jadallah said he witnessed 100 companies a week coming in seeking to be acquired by Microsoft. He left Microsoft in 1999 after being there for 12 years. But Microsoft does not buy as many companies as it used to and the price may not be what a startup expects to receive, he said.

Companies seeking to be acquired often were struggling or thought they would be a perfect fit at Microsoft, Jadallah said. But startups are better off pursuing a partnership strategy with Microsoft and taking control of their own destiny, he said.

Providing further guidance, Jadallah said ISVs should not plan to close a deal with Microsoft by a certain date. They should not plan on having Microsoft provide their first customers and they should not skip ISV programs.

What gets Microsoft's attention is when a startup has customers, he said. "With Microsoft, customers speak louder than anybody," said Jadallah.

The many ISV programs at Microsoft usually can fit a startup. "It's very unlikely that they don't have a program that works for you," Jadallah said.