I think I get where you're coming from; the cover date has almost nothing to do with when it is available on the shelves. However, if you don't use that 'metric' to classify them, then what do you use? The in-shop-date is variable and isn't on the cover. So, if you just rank them by issue number there is no point in ranking them by year... and then it gets a bit confusing.
I think you're pretty much stuck with using what is actually printed on the cover otherwise only you will know what the date means and this isn't Through the Looking-Glass.
The ones I really have a problem with are the 'Christmas' Progs. They are all wrong! I don't know who dreamt up the alternate Prog numbers, but it was a bad idea. Progs 2000, 2001, 2002 etc all the way up to 2015 should be in the previous year. Prog 2000 is Christmas 1999. Sure, they are end of year double issues, but if somebody asks me where I was for Christmas 2000 I don't think they mean 1999! Otherwise, that way madness lies!

Let's not get started on the Winter Specials though. They appear to sport the correct date, but Winter is from December to March...