I was just thinking about what games I can recall that split a fanbase of an established franchise. Here's what came to mind:

Burnout Paradise: There seems to be a major divide between those who loved the streamlined experience of Burnout 3 and those who appreciate the open world and online innovations of Paradise

Grand Theft Auto IV: The GTA 3 trilogy was one of the most acclaimed game series of last gen. GTA IV has become one of the most acclaimed games of this gen, but is also faces one of the most prolific fanbase splits. Some loved how ridiculous the series got by San Andreas, others praise the more serious nature of GTA IV.

Halo 2: Many were dissapointed by how the storyline went down, while others were too distracted by the multiplayer that set the modern standard for console online multiplayer. 

Resident Evil 4: For many, 2005's game of the year came less than 2 weeks into the year. This highly influencial game reset the series gameplay with a new over the shoulder aiming mechanic and a higher focus on action rather than adventure. Some longtime franchise fans resented that change.

Every Console Zelda Game Following OoT: If there is one thing that just about every Zelda fan can agree with, it's that Ocarina of Time was an exceptional entry in the series and a landmark moment for video games. The 3 major sequels that followed it then provided some noticable cracks in the fanbase. People seem to either love or hate Majoras Mask. Wind Wakers cel-shaded art style provided a new aspect of the series to debate. Most recently, Twilight Princess has created an entirely new split between those who dug the fan service experience it strived for while others were turned off by how similiar it is to OoT and the tacked on motion controls the Wii version included.

Other Ones

Sonic Adventure
Prince of Persia: Warrior Within
Jak II
Street Fighter 3
Guitar Hero 3
Banjo-Kazooie: Nuts and Bolts
Metal Gear Solid 2
Colin McRae Dirt
Call of Duty World at War
Rainbow Six Lockdown
Left 4 Dead 2
Deus Ex: Invisible War
SW Knights of the Old Republic 2
Super Mario Sunshine
World of Warcraft
Final Fantasy XI and XIV
Fallout 3

Definitely agree with you on Dirt and Lockdown. I played countless hours of Raven Shield and was extremely disappointed with Lockdown when it arrived, and in fact, every R6 game after that.

Sonic Adventure- I loved it...although its not a good game, I just love Sonic.

I wasn't really in to Burnout before Paradise came along so that sucked me in.

Wind Waker was awesome, again from a non-fan point of view it really drew me in.

Isn't Left 5 Dead supposed to come along and do this as well? :p

My take on some of the splits:

Burnout 3 was my favorite game last gen, and when I tried out the Paradise demo I was very underwhelmed and disappointed. However, after seeing Criterion/EA add so much free DLC and show such care for their product, I can't help but pick it up and give it a fair shake sometime soon.

I wasn't a huge fan of the original Halo, but I absolutely loved Halo 2s multiplayer. First online game I really got into.

RE4 was the first RE I played, and it was great. I also bought REmake and plan to play it sometime soon.

I also share the non-fan view towards Wind Waker, which was the only LoZ I've played to completion, and I really liked it. I adore the art style.

I was turned off by the guitar crazy direction Neversoft went with GH3 and the cashcow crazy direction Activision went with the series from there on out.

I loved the original Banjo-Kazooie, and I loved Nuts and Bolts, so thats one split that I definitely transcend.

I love arcade racers and really dislike sims, so Dirt appealed to me much more than any of the previous Colin Mcrae games.

I thought Sonic Advenure and SA2 were fine, but they don't come close to the Genesis trilogy. I think just about all older Sonic fans can agree that the series following the Adventure games took a serious nosedive.

Nice post. A controversial opinion perhaps, but I think that the gripes of series-fans seem to be ill-conceived and generally turn out to be plain wrong.

Very much agreed on Burnout.  I didn't hate Paradise but it's nowhere near what Burnout 3: Takedown was.  Best racing game ever IMO.

Another game to add to your list:  Deus Ex 2.  That game shouldn't even share a title with the first game.  Knights of the Old Republic 2 could also be on there.  A couple of upcoming games that I assume will split the fanbase at least a bit: Max Payne 3 and Bioshock 2.

Good picks.

Good picks, but you forgot Final Fantasy XI and XIV

All of the ones you did captions on are very true. 

world of warcraft... can't get over how utterly and completely they undid what happened at the end of The Frozen Throne.

I actually agree with pretty much every game there, or at least I know the split the fanbase even if I didn't agree with them.

• I love Burnout Paradise and Takedown, so that didn't bother me. Both are amazing games in their own right and I appreciated both of their natures.
• Grand Theft Auto IV remains one of my favorite games of all time, and I actually was not a big fan of San Andreas so I can see how the fanbase was split.
  
• Halo 2 is a great game and I love it for the multiplayer and co-op. The singleplayer got a bit disappointing as it went on, and, yes, the cliffhanger ending was stupid but I still like the first two to this day.
• Resident Evil 4 is also of my favorite games ever, and I vastly prefer its control style to the others. I have actually beaten the first game and most of the 2nd, but once I played the 4th it was hard for me to go back. I also like (not love) Resident Evil 5.
• The Zelda argument is true as well. I love Ocarina of Time, obviously, and I thought Majora's Mask was a unique game that I never got into that far because I couldn't understand it fully at my young age. Wind Waker is a breathtaking game and probably my 2nd favorite on the Gamecube (next to RE4) and I did not like Twilight Princess because it was too much of the same.

I will agree with everything you have posted, although I have yet to meet a person who liked KotOR 2 (out of the box, with all the gamebreaking glitches) over the original. On the Zelda side of things, I am completley mystified by the people who like the sidequest-heavy Majora's Mask over the other games in the series. But to each their own, right?

You never mentioned Counter Strike :o

Halo 2 by far. The lack of context (It's a giant plant! We will now call it Gravemind!), the lack of an ending, the lack of actually fighting on earth and the lack of playing MasterChief all of which were all soundly addressed in the single player campaign of Halo 3. I remember a ton of players being turned off by the time the credits rolled at the end of that game.

I don't remember seeing much division for Jak 2. Probably wrong. If anything I think it made more fans in the long run.

I don't remember much division against Sonic Adventure when it came out. Sure there's alot of anger in regards to recent Sonic Team endeavors, but when SA dropped on DreamCast I remember alot of fans just happy Sonic finally went 3D.
 

Banjo Kazooie: Some people loved the shift to vehicle creation, found in Nuts and Bolts, while others hated it.
Sly Cooper: Sly 1 was an excellent platform game, the second was an excellent Sandbox game, some welcomed the change others hated it.

With Gta IV it didn't "split" a fanbase at all. The sales were better then ever, and I haven't heard of many people who didn't love the experience. Maybe a couple griped about the serious story, but people still loved the game. 

Resident Evil 4 is the first one that came to mind.  But many long time Final Fantasy fans don't like XII, which is probably my favorite, even after beating VII and X. 

You can add Oblivion, Mario Kart Wii, Star Fox Adventures, and Super Smash Bros. Brawl to this list.

I would have included the CoD4 to WaW transition and said that the series went from totally awesome to absolutely terrible.

silent hill 4 

Counter-Strike people...this war is still going on today. 1.6 players against Source players has affected tournaments and even patches, and now Valve is completely overhauling the graphic system.

FFIX as well.  Those that came to the series only after VII simply didn't get it.

L4D2 did not split the fanbase,  It just angered some people that it came out so soon.  And most of those people probably own the game right now. 
  
From a genre point of veiw, Halo really split a fan base.  It caused every 12 year old wannabe power player to think they where gods at fps, and we all got to hear about it on forums.  It over simplified the genre and really alienated the hardcore fps players.  Same thing happed with CoD4 and MW2.

Definitely GTA 4.

Final Fantasy XIII, it seems. It's all a matter of patience.

I understand how your examples split fanbases, but all those games made those franchises better and evolved their respective series. 

Metroid Prime was pretty divisive. I'm a big Metroid fan, and was really skeptical when that came out. I've still only played a couple hours of it. I keep meaning to go back to it, but haven't got around to it.
 
Grand Theft Auto 3 was pretty divisive for me too. I dismissed the game for a long time (a year or more) before finally trying it. In the end, I really liked it, but the first GTA is still my favorite.
 
I still haven't played Ocarine of Time. I've played all the early Zelda games when they were new, but never owned an N64. Still haven't gotten around to playing it, but I doubt it'll replace Link to the Past in my mind as the best Zelda. Too much history and nostalgia.