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Castlevania: Portrait of Ruin. The most common complaint (that I've seen, anyways) from haters? "It's all anime-ish and crap. PoR sucks." (Most of these people also adore Dawn of Sorrow despite it having a similar art style). If you look past the "anime-ish" quality, you'll find a really fun game with a (IMO) decent story. Besides, it's the sequel to freakin' Bloodlines! Now, I do have some complaints of my own (spoiler'd due to tl;dr-ness), but they don't stop it from being a decent game (at least the main adventure).
1:Charlotte is next to freaking useless. The only thing that even slightly redeems her is her status upgrade spells and using her for Dual Crushes.
2:The alternate modes in PoR are just pure crap to convince you that you're getting more out of the game than you actually are. This is a problem with this particular Castlevania because the extra modes had almost no thought put into them and thus end up feeling phoned in (Axe-Armor Mode?! Freaking Seriously?!).
3: A specific problem with the extra modes is the Sisters' mode (the only one that seems to be thought out). What is this fatal flaw that makes me hate the Sisters' mode with the burning fires of Hell? NO LEFTY SUPPORT. Screw you, Konami.
4: Some of Wind's/Eric's quests can be easily and unintentionally missable, since certain items seem like they can be found elsewhere, but cannot (HOW IN GOD'S NAME WAS I SUPPOSED TO KNOW THAT THERE'S ONLY ONE MOLDY BREAD IN THE GAME)
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Castlevania: Harmony of Dissonance. I think what distances most haters from HoD is the soundtrack, especially when compared the quality of the music in HoD's predecessor, Circle of the Moon. It's a shame, since besides that, HoD is probably one of the best Metroidvanias (God bless Konami for the forwards/backwards dash mechanic). HoD's not quite on the same level as SotN for me in terms of my favorite CV, but it's pretty damn close.
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Fatal Fury 3. Many SNK fans I've seen dislike it because of the "complicated" plane-switching mechanic (OH GOD IT HAS THREE PLANES INSTEAD OF TWO BURN IT WITH FIRE). First off, FF3's plane-switching is not that hard to wrap your head around; it's kinda awesome here because you can't just play "Back and Forth" to run out the clock; instead, you only get about a second in the foreground/background planes (also forcing you to think faster about what to do from there). Plus, for its time, the attention to detail was absolutely badass IMO.
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Yoshi's Story. Almost all of YS' haters hate it because it's not like Yoshi's Island. Well, gee,
maybe that's why it wasn't freaking designed to be Yoshi's Island 2? (well, ok, it was called Yoshi's Island 64 in development, but they yanked that title to distance it from Yoshi's Island). It's a short game, but some of the levels can be damn frustrating, especially when trying to find all 30 melons in each level; not to mention all of the Special Hearts to unlock all the levels.
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Megaman 7. The only real problem is the fact that the sprites are HUUUGE for such a small screen, but the player should be able to get used to it fairly quickly. It's also got some great jams. Plus, the hidden fighting mode is really cool IMO.
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Megaman 8. Other than MM sounding like a little girl, I thought that MM8 was a decent adventure; only problem was getting used to the slight overhead view, but even then, you should quickly adjust to the view.
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Legend of Zelda: Phantom Hourglass (Oh shit I went there). To tell the truth, I actually
preferred PH over Spirit Tracks! I thought PH's story was stronger; the items felt more unique in PH (since their touchscreen mechanics were new then; most of the items in ST just take those items and do nothing new and special with them), and to risk an immediate execution, I felt that rolling in PH felt more natural than double-tapping to roll in ST.