It is becoming ever more popular for agencies to insist on your being paid as a W-2 rather than a 1099. Does it matter? Oh, yeah!
Sure, it's just a project. 3-months. 6-months, so evern though you're receiving a W-2, you're not really an employee, right? Wrong. The situation is temporary, but that just means you're a temporary employee. As far as the IRS is concerned, if you receive a W-2 you are an employee. There are 'test' scenarios to determine if you are really a contractor when receiving a 1099, but when you're being paid via W-2, the guessing has been removed.