I think the key point to understand is that vast majority of game writing is absolutely atrocious. Valkyria Chronicles at the very least feels like it has actual characters who develop in a proper manner, and Max's improbably supply of giant tanks aside for the most part it has a (standardfare) story that makes sense (for example the plot isn't figuratively AND literally kidnapped by the Joker like in Arkham City), and there is chemistry in the romance (which is more than, say, a certain studio that CATERS to a particular crowd obsessed with this stuff, and it comes off as, errrrr, fanservice)
For example, I'd say VC1 was more enjoyable storywise than for example Mass Effect 2.
So I suppose what I'm saying (and said ages ago) is that 99% of games have absolutely shit (or non-existent) storytelling. Doom could be the best vidya story ever if they just incorporated some manic adlib self-monologue to it in the vein of the legendary masterpiece-tier comic adaptation.
Well there is the team mascot but that's really small and something Japs cannot help themselves with, I'd jot down a negative mark on the fact that the plot above the character-level story (the ancient secrets and ancient stuff stuff) is very standard fare (though they have the courtesy of having no prophecies, my pet hate cliche when used straight), but I think overall what makes it is that the character-level story works, there's a sense of genuine chemistry with Welkin and Alicia (and the game does take its time with this), and it has a number of bits where it diverges from the default setting for stories like Zaka's reaction to the demolished Darcsen concentration camp barracks.