I encountered the multidimensional arrays issue recently. One lame method I used was (in PM 1.8.0 - it has native arrays) to have a separate array for each dimension with the indexes matched up.
haha, yes, thats what I did too. ugly and unwieldy long components list in the property inspector. good to hear about the 1.8 thing! looking forward to that.
another major major major beef I had is the sorting layer issue with transparent textures (with a 3D cam). the unity free version just cannot display multiple, layered/ overlapping png sprites without messing up the overlapping. some z buffer pro version thing IIRC. in the end i had to manually set the sorting layer AND the sorting layer depth for each texture . and there are 155 in this game.
but at least it is possible to make it work, even if its a headache :-)