What games have given you bad first impressions, only to have you enjoy them later on?

Super Mario Sunshine- I was like "WTF, this isn't a Mario game.", but it did introduce me (by random chance) to Paper Mario TTYD
Wind Waker- gave up after the "Wrong! Do it again!" design of the Forsaken Fortress. I have since gotten to the boss before the Tingle fetchquest
Majora's Mask- the prologue frustrated me on the disc and on the cartridge. Finally gave it a third chance and I am now in the snowy area.
Kirby Super Star- didn't like the DS version, but I am now enjoying it on the Wii

Super Mario World. I don't know why, but I hated it when I first played it. Now I love it!

Tbh, I didn't really like KIU at first, and it took me maybe 30 minutes to fully understand the control scheme, but I quickly caught on and enjoy it so much now.

Sega All Star Racing, I hated both the plain and boat controls, but I'm used to it now, and apart from some flaws it tramples MKWii.

Metroid Prime 2. It was so different from 1 it was a real disappointment at first, realy like it now. Even though they could never reach what they did with the first..

Amen on the controls. Wish they'd just made it traditional. Why does Nintendo like the stylus so much?

Pokemon: I didn't like the design of Diamond and Pearl at a demo. I then played Soulsilver and I love it.

Unlike most games that abuse the stylus (lolol Zelda) this game actually benefits a lot from it. The CPP doesn't offer enough speed (though it still should've been included for slow platforming sections). If you have one, try moving with the face buttons and aiming with the stick.

But yeah, Kid Icarus: Uprising took about 10-15 minutes before I really enjoyed it. And even further past before I truly loved it.

Also

GoldenEye 007 - Took long to get used to the somewhat shaky Wiimote controls, and GC doesn't offer enough speed for multiplayer.
X-Scape - (Why is it that games I love never get the best first impressions) The tutorial felt really drawn out, and the stylus controls sucked (buttons were better)
World of Goo - (another example of this) The first few levels were too easy.
Bionic Commando Rearmed - Only because the X360 controller is a joke, especially the D-Pad. PS3/PC were much, MUCH smoother.

I used to have a list of games I hated within the first hour...I don't have that list anymore, and I don't remember all of them, but here it goes:

Banjo-Kazooie (I played the demo, thought it was too cutsy and the collecting seemed to take precedence over the platforming)
Final Fantasy VI (It is soooo slow at the beginning. No matter how many times I play it, that first hour always bugs me)
Secret of Mana (First boss fight still ticks me off. Even the second boss isn't as cheap)
Golden Sun (So many textbook examples of bad writing right at the beginning. It gets way better soon after, but that begining killed it for me the first time I played)
Wind Waker (I sold it when I couldn't get through the very terribly designed Stealth section near the beginning)

There are sooo many more, but I can't think of them at the moment.

Majora's Mask. The first time I placed it wasn't a good experience, because I was two days into my first cycle outside of Clock Town, and just when I was saving at an Owl Statue, the fuse in my Wii's power cable broke... Two hours of gameplay gone... So I just gave up on it.

Six months later I gave it another chance, and it became my favourite game of all time (despite the annoying save system).

Metroid:Other M. I didn't like it at first, because having so little health made advancing through the game very difficult. Then, I found my first energy tanks, the game became much more manageable and I started having a lot of fun.
Shinobi 3D. I played it on easy and made it through the game by abusing the infinite lives and infinite continues, without even trying to get good at it. I liked it, but considered it mediocre at best. Then, I gave a try to the normal difficulty. I lost often, but got better the more I played and felt rewarded for my effort every time I cleared a stage. I believe that the higher difficulty made me learn the game and appreciate the multitude of moves you have in your arsenal. In the end, I discovered that it is far from mediocre- now, I consider it a great action/platformer.

Majora's Mask is the first one to that comes to mind. I hated the time mechanic when I started it. Now, It's one of my favorite games of all time. Second only to Skyward Sword in my Zelda rankings.

Well, the stylus controls in Kid Icarus: Uprising help you keep up with the fast paced combat.

Pikmin is the biggest one aside from Animal Crossing to come to mind. I didn't expect so much from a Nintendo RTS game. Probably one of the best games I've ever played.

I'm serious when I say this: I love the controls now. I'm just saying it took me a little to get used to them. Unfortunately there are some people that won't play the game because of the controls, even though you can change them and, tbh, after the first half hour, you'da thought I'd been playing for days, the controls are really easy to adjust to imo.

Call of Duty 4. I liked the first 2 games but the overhype on this game just kinda annoyed me. But despite that, Call of Duty 4 is one of the best examples of the type of FPS it is. Which made Modern Warfare 2 all the more dissappointing.
Metroid Prime: LINEAR FIRST PERSON INTRO ON GENERIC SPACE STATION. People seriously gave up on the game just because of this, which granted is dumb, but despite clearly trying to be like the intro to Super Metroid, just fails at getting across almost anything people like about the series or the rest of Prime for that matter.

Good thing the game gives you infinite life against that first boss, then?

Yoshi's Story. I was confused as to how I was advancing so quickly. Turns out it's not about beating the game, but rather beating the game well.

It's not infinte. Only about 3 or 4, I actually Game overed once because the game doesn't explain the gameplay to you at all, and I didn't have a manual.

Suikoden III - I was initially turned off by the clunky battle system and, to be honest with myself, the meh visuals. While I still never did anything more than tolerate the battle system, on my second attempt to play it I quickly learned to love the enormous cast of compelling characters, the many plot threads, the war battles and the Trinity Sight System. And trying to find the absolute worst characters to star in plays at the castle's theater was delightful.

Metal Gear Solid/The Twin Snakes - I think my biggest issue, in hindsight, was simply that I kept trying to play it on a television that was too dark, so I couldn't tell half of what was happening onscreen and I was always incredibly frustrated by the time I'd left the first room. A few years later, once I had a better TV, I gave it another shot and instantly fell in love with the stealth gameplay and the awesome ridiculousness of the story.

Chrono Trigger - I'm not totally sure what changed with me. For whatever reason, it just didn't "click" with me the first couple of times I attempted to play through it, but now I can't imagine not liking it.

The Legend of Zelda: A Link to the Past - It's similar to Chrono Trigger, in that I'm not terribly sure what changed from me "not liking it all that much" to "liking it a lot". Maybe my tastes changed, or I got better at exploring the overworld.

Oh yeah, that's another one for me...and like you, I'm not sure what happened to change my mind...