What the subject says.. Which are the most underrated game franchises ever? I have 3 franchises that I consider to be pretty damn underrated!
1. Contra- Contra used to be a popular franchise back in the 80s and the early 90s along with Mega Man, Castlevania and others. Sadly, when the PSX generation began the franchise started to get ignored really badly thanks to disasters like Legacy of War and The Contra Adventure which got awful reviews. Things started to get better with the PS2 generation thanks to games like Neo Contra and even better with the 7th generation thanks to Contra 4 and Hard Corps: Uprising.
The newer games are pretty awesome! I love Contra 4 and Hard Corps Uprising is one of my favorite XBL/PSN titles, but sadly the franchise is becoming more irrelevant with each passing generation and it looks like Konami doesn't even want to make another Contra game..Heck.. They teased something at E3 2011 and then nothing! Oh well. It was fun while it lasted! 
2. Klonoa- I was looking at the " Help with the PS1 collection" thread a few days ago and then I saw Klonoa get mentioned. I had a huge smile on my face at that moment. Why? Because Klonoa gets so little attention nowadays I am just ahppy to see someone give the props it deserves! Klonoa 1 and Klonoa 2 are really fun. The graphics are pretty nice, the games are charming, the platforming is fun and fair ( for the most part), the difficulty balance is perfect and the plot is simple, yet good!
The first game also got a remake on the Wii, so I recommend you to check out the remake if you haven't already! Trust me, it's going to be worth your time and money! 
3. Earthworm Jim- The first two EWJ games were so damn awesome, charming and funny! Specially funny! Then the 3rd game happened and things got UGLY! It lacked the charm and humor of the first two games and the gameplay got screwed thanks to slippery controls/awful camera ( that is saying a lot for a platformer that came out in 1999, 3 years after Super Mario 64 and a year after the first Banjo-Kazooie!) and dull levels that don't allow you to explore at all ( again, Super Mario 64 and Banjo-Kazooie)!
In 2013, EWJ creator Doug TenNapel teased a possible 4th Earthworm Jim asking if it should be named EWJ3 or EWJ4 since he didn't consider the atrocity that is Earthworm Jim 3D to be part of the Jim universe. It was obvious at that point that he had some ideas for a 4th EWJ game in mind, so maybe he started working on the game in the meantime!
---Member of the official Squeezol Fanclub---
