To be honest I don't really care that much about what "the developer had in mind". I'm in for my personal enjoyment after all.
I just tend to enjoy Japanese games more with their Japanese voice acting. And yes, I think the Japanese voice acting in these games is better in most of the cases, or to be more specific, it is more to my personal taste. That may very well be due to the fact that my Japanese is much worse than my English, and as such I don't notice the shortcomings. But even knowing this doesn't change the outcome, which simply is that I enjoy the Japanese version more.
There's one thing I often notice in dubbed Japanese games though (regardless of the quality or flaws of the Japanese voice acting): The English voice acting in these games just is.. different than in most other western games. I'm not even sure if it's down to the choice of voice actors itself or if they're told to speak in certain way. But it just strikes me as odd.
Of course there are exceptions to the rule. For example, I liked the English voice acting in Xenoblade Chronicles which fit pretty well.