Excellent emulator, however it still has many flaws. In Megaman Battle Network (entire series) the save file (battery save) can corrupt on its own. I am not the only user who has experienced this, and it is terrible considering you could have a game consisting of 60+ hours of playtime and you would lose it all.
Certain games still have graphical glitches, for instance Dragonball Z Legacy of Goku II and Megaman Battle network 4, at least in my experience.
If it is possible for you, you could consult the source of VBA-link to implement wifi linking. Considering this being possible of course.
Finally, another factor is your lack of development. The last real "update" for this application was 29 May 2011. Which makes it seem as if the development for this is either dead, or it is thought to be complete/ perfect - which it is not.