AKA: Prognosis Negative!
The core strength of the Lone Gunmen (the characters, not the show) is the same thing that I think makes it hard to base an entire show around them; Their group dynamic. While they can be quite an entertaining trio, bouncing off each other and bickering, the additions of two new characters will, definitionally, alter that dynamic. I would say the dynamic has been altered for the better, but I can imagine the writers, who were probably fans of the characters on The X-Files, might want to see the original dynamic play out a little bit.