All right, time for me to reveal who I think are the most underrated Mario characters.
Mario
Mario may be the mascot of the series and representative of Nintendo in general, but honestly, a lot of fans treat him like crap. They call him a "lazy, good-for-nothing, fat ass" (and the fat ass remark proves they've never seen Wario or Dr. Robotnik/Eggman). Even worse, people consider Luigi to be the smarter brother which makes absolutley no sense at all considering Luigi is incredibly gullible. Just look at Super Paper Mario, "I don't give my name to scoundrels! Luigi to the rescue!" or something along those lines and let's not forget the mansion he "won" in that contest, even King Boo states "Who would believe mansions get given away in contests? Talk about gullible!" Plus, I've read some stories where Mario's a brain-dead idiot and some graphic artwork of Mario being defeated by Bowser. I don't want to go beyond this. However, I do agree that Mario's spent a little too much time in the spotlight and could use a little vacation.
Daisy
A lot of people hate Daisy. Why? One of two reasons:
1. Excluding Super Mario Land, she's only appeared in the spin-offs.
2. "HI, I'M DAISY!"
Those are both incredibly stupid reasons. So Daisy's only appeared in one mainstream game. Big deal. She's still appeared in more mainstream games than that failure of a Luigi clone. Plus, Daisy's stats in the spin-offs are pretty good, unlike this creature

Also, Daisy is unique among the female characters in the Mario series as she's a tomboy instead of being a stereotypical girly girl like Peach (sorry, Peach fans didn't mean to diss Peach, just using her as an example). As for the "HI, I'M DAISY!" thing, that was is ONE...FREAKING...GAME. Is ONE catchphrase in ONE game really worth a lifetime of hate? Also, I'd like to point out that the only reason Daisy says that is because YOU as the PLAYER make her say that.
Donkey Kong
While DK's not really hated as much as the other characters I've chosen for this thread, he is pretty much non-existent. I've read plenty of fan fiction for Mario, but I've never read a where DK was the star except as a special guest star.
Bowser Jr.
Bowser Jr. is incredibly hated, especially by koopaling fanboys/girls. People say the koopalings are more unique than Bowser Jr. Well, take away their names and physical appearances, and they're all the same. The Koopalings all copy each other: "Oh, I'm gonna use my Airship to conquer a country and steal the King of the Country's magic wand, turn him into an animal and wait for Mario to show up and kick my butt!" Bowser Jr. is actually capable of using different strategies each time he faces Mario.
Sunshine=Giant robot, magic paintbrush, and Mario disguise.
New Super Mario Bros. DS=hide in towers and castles and fight Mario directly
New Super Mario Bros. Wii= wait for Mario to show up and attack from the Clown Copter (I know Bowser already did this, but it was in a different game, unlike the koopalings who all use the strategy in the same game).
Galaxy and Galaxy 2=Return to using giant robots but with different strengths and weaknesses.
Also, going back to the uniqueness argument, the koopalings may look unique, but they don't have any personalities. Bowser Jr. on the other hand, likes art evidenced by his magic paintbrush, he likes playing sports, and he apparently likes Bullet Bills since his kart in Double-Dash looks like a Bullet Bill and that was Mecha-Bowser's main form of attack in Sunshine.
Goombario
Out of all the original Paper Mario party members, people claim that Goombario's the least useful which I couldn't disagree more. Goombario's Headbonk does the same amount of damage as Mario's Jump.
Jump=Headbonk
Super Boots=Super Rank Headbonk
Ultra Boots=Ultra Rank Headbonk
Plus, if you're willing to give up one turn using Goombario's "Charge" ability, he becomes even stronger. As for his "Tattle" ability, there was this one idiot on YouTube who commented that they preferred using the Peakaboo badge as opposed to Goombario's Tattle because they don't want to waste 1 FP to find out the enemy's HP. What the hell? Goombario's Tattle doesn't cost any FP and he actually tells you the attack, defense, and possibly some strengths and weaknesses about the enemies. I don't see the Peekaboo badge doing that. Myself, I find Goombario to be a very good partner as I've taken down some of the toughtest bosses in the game with him. (Huff N. Puff, The Master's first 2 forms).
O'Chunks
There aren't really a lot of Super Paper Mario fans and the few people who do like Super Paper Mario are usually attracted to Dimentio because they think he's epic, Mr. L just because he's funny and he's Luigi dark side, and for whatever reason, Mimi. From my POV, O'Chunks doesn't really get any love from the fans. Personally, O'Chunks is my favorite member of Bleck's army due to his code of being an honorable warrior.
Mallow
People often hate Mallow because of his crybaby personality when he first gets seen. Do those people even realize how boring a game would be if everybody was a tough, macho, fearless warrior? That's pretty much why I put Mallow on the poll.
Anyway, I think that's enough for now. I'll give my reasons for the rest of the characters later.