One way to help with the Shaman's pathing would be to use the waypoint feature. Shift+right-click a few times and the shamans and boats will follow the path.
I have seen the AI move units around with transports, sometimes (rarely) on Frost Islands, but particularly on Fallen Moon. That might be because those are the only maps where moving by water is really useful. Once, the sneaky AI came around the far side and sent units up to capture parts of my completely undefended base while I was busy managing the front line on the ground elsewhere, the cheeky little...
I agree, hats off to the strategy map AI. I saw how it was before the patch, and this is MUCH better now.
