Perhaps the most compelling and revealing detail here is the type of graphic being trademarked. As pointed out by other neoGAF forum users, its style appears to match that of the controller graphics featured on the top of the NES Classic and SNES Classic packaging (check out the top of the box in the photo above). However, big tech companies often trademark and patent things they never intend to make in an effort to protect themselves from competition, which may be the case here (or who knows, the trademarks may be for something else entirely). Though considering the SNES Classic console was long rumored to follow the NES Classic, and that proved to be true, there is reason to put some faith in this speculation about the N64. If a N64 Classic does get announced and hit the market, expect stock to be slim and availability limited (that just seems to be how Nintendo handles these things).
It's tough to know exactly what is in Nintendo's pipeline, so for now the best you can do is brush up the GoldenEye 007 cheats and hope for the best.