What alliance did I miss
You didn't. It's a lot easier to tell if you differentiate between player nations and NPNs. You could maybe make two maps, but I personally liked the old system a lot better. Again, I will reformat the OPs and the NPC nation list to look good and take up less space, as well as clearly indicate what group is what.
The second issue is united joint alliance chains.
This is like listing A, B, C, D, E as one alliance, and E, F, G, H, I as another. Obviously, A through D would be one color set by shade, and F through I would be another color set by shade, but the E nation would be a joint party in between. What color would E be, then? With three or more groups, this can make things really convoluted.
I personally see the current alliance map as convoluted as is, and it could be even worse with more sides involved.