I think one of the major problem is all those poor A1200's that are butchered to be badly fitted in various tower cases that were not meant for that... I've seen some horrendous job around, so in those conditions it's no wonder the motherboard suprisingly break down quickly... I reckon Commodore A1200's are good quality build, as long as you don't tinker with them to much and keep them in their original case (where they're meant to be!). I've one here I got on a car boot sales which was in a *really* bad condition (all rusty inside, looks like it was kept somewhere wet and dirty for a long time), on top of that it made four flights in the luggage hold (you probably know how careful are the luggage handlers;) and it's working like a charm.
Another explanation for the decreasing availability of A1200 might be all those numerous pseudo-collectors who are buying some Amigas just to have them, but never use them beside the odd game from time to time...