Having the same problem.
I haven't seen anything beyond the train station in the beginning yet, but Barret, Biggs, Wedge Jessie, the guys in red and the Shinra soldiers are all stuck as chibi polygons.
And Cloud's battle model is the default as well, so it seems like the Battle Models mod isn't working either.
Have followed the load order in the written tutorial, triple checked. Don't know what the problem is.