The only downsides to independant tanks are:
2) If you do have to shut down a tank then you have just lost access to maybe half you gas.With manifolded doubles you would still have access to all of it. Again not a big problem on NDL or limited limited deco dives.
I am assuming you mean shutting down the reg on that manifold post. If you shut down the tank, by the tank valve, you would not have access to the contents of that tank. And, if it were a free flow, you probably would not have cured that problem either (by shutting the tank valve, versus the manifold post). Is this correct? Can you shut down (isolate) a tank on the manifold? Or, you only isolate the regs on each side from one another? Or both? I'm don't have any experience with doubles or twins - yet.
In any case this is a good point and one that I didn't think of. I don't think it will be a major problem for my Recreational Diving though. It will just be something I will need to take account of during my dive planning. If I do get into Tek Diving, I'll end up get a full manifold setup, and probably the tanks won't be AL80s.