I'm not sure exactly sure about the reputation of some of them, but here's all who I can think of:
Big the cat - From the Sonic series, first introduced in Sonic Adventure. I find him funny and not at all annoying. Also cool that he's just so different from the more recent overly anime or even DBZ inspired characters.
Tingle - From the Zelda series, first seen in Majora's Mask, though his Wind Waker form is my favorite. By extension I also like Purlo, but people don't talk about him anywhere near as much.
Fi - From Zelda: Skyward Sword. I do think there is a problem with her popping in every 2 seconds to tell the obvious, but I feel that's more to do with bad game design than it is her character. Others say she "has no character", but that's really what she's supposed to be; a robot or computer. At the risk of maybe spoiling a bit much, something she says to Link towards the end of the game hints towards this greatly. I also feel it's supposed to contrast Ghirahim's more extreme emotions.
Samus - Well, not exactly. I guess people hated the way they characterized her in Metroid: Other M. I didn't feel much one way or the other, but I found it believable and thought it was their right to make her however they wanted, with no real set character made in any of the previous games. People talk about it being sexist or her being made into a cry baby, and I just can't understand any of those arguments. Her relationship with Adam reminded me of the one between Snake and the Boss from Metal Gear Solid 3, of which, so far as I know, nobody complained about.
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About suffering they were never wrong,
The Old Masters: how well they understood
Its human position; how it takes place
While someone else is eating or opening a window or
just walking dully along...