I might be wrong but I think every club in the AFL now has a reserves/affiliate second tier team that they have either complete (reserves) or substantial (affiliate) control over.
I have to confess to not knowing a lot about the Victorian clubs' arrangements with VFL affiliates, but as far as I know the last dominos to fall were the Perth sides having affiliates in the WAFL, which happened in the last couple of years, and the SA teams having reserves sides in the SANFL. This year is the Crows' 3rd year in the SANFL - the Crows having been a club created in 1990 specifically to play in the AFL as a representative of all 10 SANFL clubs of the time. One of those clubs, Port Adelaide, entered a team in the AFL a few years later but the SANFL club remained in the SANFL and was not actually a reserves team for the Power until the last few years. It created a bizarre situation where the Crows would draft players from interstate - they would be farmed out to SANFL clubs via a "mini-draft" and some young Crows would end up deep in enemy territory playing for Port Adelaide in the SANFL.
As others have said, I think the reluctance of SA and WA to have "AFL reserves" teams in their local leagues is largely historical - these are once proud leagues that were comparable to the VFL of the time (which has now expanded into the AFL) and there are many people, particularly those who were into adulthood before the Crows came into the league in 1991, who still feel a greater parochial attachment to the club they grew up supporting than the one that was created from thin air to compete on the national stage. Indeed, there is a very strong school of thought amongst SANFL die hards that the two AFL reserves teams should be kicked out of the SANFL.
As others have said, a full AFL reserves competition is definitely desirable and probably inevitable.
Now, let's have a good clean game and we can all join together in hurling vitriol at Kurt Tippett.
I might be wrong but i think north still splits its affiliate sides, saint kilda has no control over sandringham (which they are parting ways with after this season) and its clear from the way melbourne play that the scorpions are an affliate in name only and don't give a * about developing youth for the dee's.