In my experience, if you want the fleece to stay as close to new as possible, you do have to keep it out of linty laundry - that would mean washing microfleece items separately, or only with non-linty covers.
BUT, that is just too much for me, so I bit the bullet and started washing everything together. Yes, there's some lint on the microfleece, but after the initial linting it actually gets better and the diapers are just fine. If I have something brand new and very linty to wash, I try to do it away from the microfleece for a wash or two to get rid of the big lint-shed before washing it with pockets.
BUT, that is just too much for me, so I bit the bullet and started washing everything together. Yes, there's some lint on the microfleece, but after the initial linting it actually gets better and the diapers are just fine. If I have something brand new and very linty to wash, I try to do it away from the microfleece for a wash or two to get rid of the big lint-shed before washing it with pockets.