Its hard to agree when it has been touted the first real exclusive AAA title worth owning the PS4. It was literally hyped all the way to its release. It was talked about a lot as being a show piece for what the PS4 can do.

F-Zero is really underrated in my opinion. It offers a very different, but equally satisfying racing experience than Mario Kart.

Sony: Sly Cooper or Starhawk
MS: Viva Pinata
Nintendo: Earthbound (People praise it, but it's still just a vocal minority)

Sony - ?
Microsoft - Banjo Kazooie (Underrated by Microsoft)
Nintendo - Advance Wars

Idk about Microsoft or Sony but fire emblem is super underrated in my opinion, for a fairly well known franchise its sales are awful.

Microsoft - Konkers (since rare got sold)
Nintendo - Kid Icarus
Sony - The Legend of Dragoon

Funniest thing I've read on here in a good minute  

Anyway: 

Sony: Sly Cooper

Nintendo: Fire Emblem

MS: Perfect Dark

Pikmin, Metroid and Fire Emblem, especially the second one, are masterpieces, yet they sell like crap.

Microsoft has dropped Age of Empires into the dust for the last ten years. Online is crap, II HD is full of bugs and now that Castle of Siege... what have you done with the series, Microsoft? You are just killing my childhood and the potential of the franchise.

Sly Cooper is really underrated for me, it really has good humor and it's actually kinda fun. Not the best platoformer, but the whole package of the series is really good.

Hyped as Sunset Overdrive is hyped. Which imo will not sell as much as it deserves.

But really the main issue from me was that you grouped Infamous with God of war (5m seller 90s  meta usually), Pokemon (10m seller high 80s meta usually), Gears of war (5m seller 90s meta usually). Infamous isn't even close unfortunately.

Do second parties count???
If so, Nintendo's most underrated franchise is Art Style...
If they don't count, I would probably go with F-Zero or Star Tropics...