Over on Reset Era, a user by the name of ReyVGM has offered a rather interesting tale supported by an unnamed source who supposedly works for Konami. So, based on all of that, we're recommending everyone ingest this information with a rather sizable grain of salt.
According to the post, when the Wii's Virtual Console went live, Nintendo sent out a list to all third party developers asking them which of their old-school games they would like to see a focus on for reissuance. The source claims that a clerical error is to blame for Contra and Konami's Genesis games never making the cut, as someone apparently forgot to give those games a checkmark before sending the list back to Nintendo.
The claim goes on to state that years later, someone working at Konami attempted to resubmit the list in order to include the missing titles but, before that could happen, said person was no longer in a position to go forward with their efforts. We aren't sure if that last bit is a real low-key way of saying the person no longer works at Konami, but we can't imagine what other reason would make them no longer able to make the request.
Oh, dang, do y'all think it was Kojima? Did Mr. Metal Gear just really want to play some Contra but, before that could happen, he split with Konami? Or what if his attempt to get Contra on the Virtual Console is the real reason Kojima and Konami had such an ugly falling out? (For clarity's sake, this is 100 percent for yucks. We don't actually believe this, though we'd certainly be up for reading some fanfic about it.)
Again, there's not a lot to hang our hat on with this, especially since we're still unclear how Nintendo officially decides what games end up on the Virtual Console and which ones don't. The original post states that this is also the reason Contra was not included in the NES Classic, but we have a hard time believing Nintendo wouldn't have reached out to Konami again, all these years later, and double checked to see if they still wanted some of their games kept out of the running.
The comments on this post range from skepticism to frustrated acceptance. The only thing we know for certain is that, if this is really how it all went down, that's an absolute shame. Also, if true, hopefully this encourages someone at Nintendo or Konami to correct the error.