Probably overthinking a goofy anime game franchise but I find it interesting that they'd choose to combine Germany and Russia into one aggressor nation for their WWII facsimile 
I can't really call it liberal anti-communist brainworms though since the East Europan Imperial Alliance is more reminiscent of Imperial Germany than anything and I think the devs were consciously avoiding depicting anything even close to fascism or communism because Sega didn't want their wholesome anime WWII game to be political
spoiler
That didn't stop them from writing in a distrusted and hated minority that was sort of a stand-in for Jews though
I was looking for PSP games to check out and remembered Valkyria Chronicles went PSP exclusive after the first game. I played the first Valkyria Chronicles when it was released on PC a while back and while I enjoyed the turn-based tactical gameplay I sort of hated the game's aesthetics. I'm sorry, but I can't take your story about the horrors of war seriously when it's depicted in bright pastel colours and when everyone involved looks like a Pokemon trainer. Plucky child soldiers is also one of my most hated anime tropes
It was more of a joke, but yes, you're absolutely right, Eastern Europe has always been othered when it is convenient for western Europe to do so. It's almost like all these racist terms are all completely arbitrary or something!