I prefer separate stables as my boy has COPD and needs lots of fresh air. Also, if there are any nasty bugs going about ie: strangles, its easier to contain.
I have internal stabling, but not american style stalls, I have a central railed pen deep littered that the 2 ponies bunk down in, then a 20X25ft stable for the 37 year old, a standard stable next to it for the Tb with a spare stable behind the ponies.