Overrated Third Party: Fifa Series (EA), GTA Series (Rockstar), Madden Series (EA), Epic Games.
Underrated Third Party: Prince of Persia Series (Ubisoft), Sonic Series (Sega).

Overrated Nintendo: Metroid Series, Wii Series, 3D Mario Series.
Underrated Nintendo: Pikmin Series, Luigi Series (Luigi's Mansion), Mother Series.

Can't comment on Sony or Microsoft, but I genereally dislike Microzoft franchises, and also think stuff from Team ICO don't get enough sales.

In my opinion the most overrated franchise is GTA. I just don't like sandbox games and playing as a bad guy isn't my cup of tea either.

In my opinion the most underrated franchise is Panzer Dragoon. I love them all, expect the one for Game Gear. Panzer Dragoon Saga is one of my all time favorite games and was my favorite RPG until Mass Effect 2 and even then it's a close second.

If you have ever enjoyed a JRPG I recommend geting yourself a Sega Saturn or a Saturn Emulator and playing Panzer Dragoon Saga asap.

Sorry, but I can't think of enough examples to fill all your catagories.

I might get flamed for this but I think Portal 2 was kinda over rated. Was it fun and witty? Absolutely. But not much replayability to it, and the puzzles were much easier than in the first one and tended to repeat alot.

The most overrated franchise of this generation has to be Halo in my book. I just don't understand how it's (still) so popular. I understand why the first two were so popular on the original Xbox... besides being the only real notable exclusive games on the system, you had the best local multiplayer since Goldeneye in Halo 1, and Halo 2 was the first breakout online multiplayer console shooter. But everything since then from Halo 3 on has been the SAME EXACT SHIT, just with even more annoying 13 year olds online, and the gameplay feels slow, clunky and dated compared to most other modern shooters.

Most overrated franchise of all time? Final Fantasy easily. Except for II (IV) and III (VI) on the SNES, there was nothing to write home about the franchise pre-VII. Then in 1997 most gamers who never even heard of the FF series jumped on the FFVII overhype train, and that along with the anime boom of the late 90's and early 00's here in the US helped propel the series to stratospheric heights despite the "gameplay" becoming more linear and uninspired with each release, culminating with the dud that was XIII.

Overrated 3rd Party:

GTA
CoD
Medal of Honour
FIFA
Battlefront


Underrated 3rd Party:

Dragon Quest
Tales of ....
Rune Factory
Little King's Story
Blazblue
Tatsunoko vs Capcom
The World Ends With You

Overrated 3rd Party - Call of Duty, Fallout
Underrated 3rd Party - Just Dance, Gundam, Dragon Quest, Harvest Moon Rune Factory, Ace Attorney

Overrated Nintendo - Metroid Prime and Eternal Darkness
Underrated Nintendo - Animal Crossing, Fire Emblem

I won't say Zelda or Final Fantasy are overrated just because of a couple of recent failures (well, failures to match the previous levels of quality) like Twilight Princess and Final Fantasy 13; especially when the old games in the series are still excellent; and games that are over 10 years old are better than nearly all of what is being made today, and not just in the Epic Adventure and RPG genre. I recently re-played FF6, 7, and 8 on PSN and VC, along with Ocarina of Time 3D, and these games I find are all more fun and MUCH more satisfying than today's traditional games in general.

total War series deserves more sales.

I'm sure I forgot a lot.

Overrated 3rd PARTY: COD series (They only made one good game)
       Final Fantasy (They Only made 2 great games (6 and 9) (8 and 10 were decent)
       Elder Scrolls series
       Fallout Series
       Madden series
       GTA Series (Only Vice City and San Andreas, were worth playing through)
       Castlevania series
       Portal series
       Half Life series
       DOA series
       L.A. Noire (we'll see what happens with the next game)
      

Underrated 3rd Party:

        Tales Of series
        Vanquish
        Armored Core series
        Bayonetta
        Blazblue series
        King of Fighter's series (Minus 12)
        Guilty Gear series (minus Asuka)
        Star Ocean series

Overrated Microsoft: Halo series
      

Underrated Microsoft: hmmmm

Overrated Nintendo:

Animal Crossing
Zelda series
Metroid series (Except for the ones that were sidescrollers)
Pokemon series (Even though I love the series)
                   
Underrated Nintendo:

Fire Emblem
Golden Sun series

Overrated Sony: 

                Infamous series (Kind of)
                Jak & Daxter series
                Resistance series

Underrated Sony:

   Valkyria Chronicles
   Hot Shots Golf series
   ZOE series
   Patapon series
   Wipeout series
   Heavy Rain