Ciao
although it might sound a bit odd if not silly, I'm displeased about your experience. Actually, while FM3a has effectively some of the issues you listed, I've never thought they were enough to part from it, even if I can still shoot with other film cameras depending on my mood.
After 1 yr and half I use it, this is what I found. FM3a, if anyone could ever do it, might be improved only in three salient points.
1) Spot-meter. Would be truly great and the only thing turning it into the ultimate MF camera ever. Maybe next FM3D (Thom Hogan is hoping for that just as I do) will have that, as well as a batteryless operating mode (exposure meter and electronic for every shot recharged by the cocking lever thumb motion... would be smart, isn't it? - actually a stiffer motion might be even nicer to deal with)
Yes, in case of strong contrasts between the center part and the sides of the frame you may pay more attention than elsewhere but in the end I never got results that bad....
2) The analog light meter should be placed on the RIGHT side, not the left. When camera is in portrait mode, it necessarily falls in the bottom ( = darker ) part of the frame and you may not see the time at all.
3) Focusing collar with prisms and hair split line: actually the best I saw so far is Leica's R8/9 but overall isn't that bad. It could just be improved a bit.
On the other hand you have a very versatile camera with also a fill-flash button and a quite nice set of features while having less buttons than other cameras - a cleaner design. Besides, a well-kept silver FM3A has much more appeal than many other cameras and equal reliability.
Where I do not agree is size. I have a picture where Zeiss Ikon and FM3A are side by side and the only difference between them are lenses, both 35mm from Zeiss. Look for yourself.
>>> Note that it's NOT a picture of mine, it's by Mfogiel (another member here) and I have always kept it just for comparison purposes. <<<