Personally, I would separate immigration in Quebec from that in the rest of the provinces. It also has to be said that far more files regarding immigration to Quebec are being processed than those concerning francophone immigration to the other provinces. I wouldn't create two departments, but I would separate the files of people wishing to immigrate to Quebec from those of francophones wanting to immigrate to other provinces.
Personally, I'm a francophone, and the federal government took two years to process my immigration file.