|Has his diet changed at all? Usually the transition to solids means more staining (the stains are usually darker and more difficult to get out, even with sunning). Or maybe a new medication or something?? Or have you changed anything at all about your routine? Like maybe from wet to dry pail, or going longer between washes?
Anyway, yes the stains should fade away over time (of course that doesn't mean you won't get new ones in the meantime). I'd try sunning them, the sun really works miracles with stains. It's hard to believe but it's really true. You could also use a liner of some sort, like a fleece liner for example. It'll help keep poop off the diaper so help prevent stains from happening in the first place. It also makes poopy diaper cleanup easier and acts as a stay-dry barrier. Doing a cold pre-rinse can help as well, as hot can help set stains more. A wet pail might help a bit but honestly I think that's way more trouble than it's worth. Some do soak only the poopy diapers, that might be an option that's a little less troublesome. Rinsing/dunking/spraying the diaper really well might also help.