There are dozens of possible reasons for Neplesia to be angry at Yamatai. For one thing, the whole bit about saying Neplesians either had to switch out of their bodies or quit the military probably meant a lot of Neppies left the army rather than become a Yamataian, and thus were out of work and quickly sunk to poverty, especially in a place as nasty as Neplesia.
Because I know the "Well, they could have just stayed, it's not Yamatai's fault" defense will be used, Neplesians are intensely proud. Asking them to give up their flesh, and if they were veterans, all their pretty battle scars, they wouldn't have handled it too well. Look what happened with Miles on the Sakura.
Another thing is the fact that Yamatai's culture is extremely alien to the average Nepleslian. Try growing up in chaos with industrial machines going constantly and incessant gunfire keeping you up at night, then going to a Yamataian city like Kyoto, with it's extremely low crime rate (I'm sorry, no crime is impossible without 20-to-1 police-civilian ratio, especially with such a large population of well-trained military personel as most Yamataian population centers are bound to contain.) would make a Nepleslian feel rather uncomfortable.
My final reason has to do with the wealth and prosperity of Yamatai compared to the mass poverty and ruin that is Nepleslian civilization. Considering the fact that Neplesia dutifully served Yamatai for decades before succeding, they got few benefits from them. While there may be over-reaching things that Wes and the more experienced players know about, I'm sure some average Nepleslian guy sitting in the projects, thinking about intergalatic politics with a bottle of cheap malt liquor in hand, comparing his life to the beautiful and rich cities of Yamatai like Kyoto, he probably thinks that he and his people got boned.
*Jumps off soapbox, picks it up, exits stage right.*