Edit: I'll accept the idea that I'm doing something wrong, but I can't put a finger on it. 
 
I loved AC2 to death. The controls weren't perfect and getting Ezio to do precision jumps can lead to frustration, but I enjoyed it because I liked climbing builds and stabbing people. No doubt after reading the GB review and other outlets of praise, I saved up enough money to by Brotherhood ASAP.....and I'm not enjoying it.
 
This is going to be hard for me to explain, but bear with me. Most of the games missions revolve around tailing and killing a target without being detected. Great! I love stealth! The problem is that the game seems very scripted on how you can do this. It seems if I go out of line I have to do it over. One mission had me tail a banker. My first though was to stalk him via the rooftops and chase him down. The buildings dead-end and If I were to jump down, I would get detected and have to start from the checkpoint. The "correct" way of doing it was to hire prostitutes and try to blend in with the crowd.  Then you send in your assassin's to take care of the remaining guards very quickly.  It seems like I have to start over because the game says so. Assassinate a guard the wrong way...automatically detected. I don't mind losing in games because I like to learn from my mistakes, but when I fail to see the mistake I did, I get frustrated.  
 
When the game asks you to be precise and presents a time limit, it gets frustrating. When you get to plan and have freedom in what you do, the game shines. Sadly, this is very rare. There are many other frustrations that are hard for me to describe at the moment. The game also has a hard time communicating with the player at times and the draw distance when running is really bad and many other small problems that get in the way ruin this game for me.      

Brotherhood made me realise that AC isn't actually a very stealthy game. Getting 100% in soe of the missions was stupid and had to follow a very specific path. I wouldn't go as far as saying it's weird, but not really how it should handle itself.

I agree all the way. I didn't love AC2, but I enjoyed it nonetheless. Brotherhood really didn't do anything for me, mainly for the reasons you specified. I really hated the whole "100 percent" synchronization idea as well, because it was even more restricting. It boggles my mind that the GB crew loved this game so much. 
 
By the way, I don' know how far you are, but the last two DNA sequences are terrible. Absolutely awful. So, just be ready for that. 

I honestly never ran into those problems, if there are rooftops to take you can take them (unless the 100% synch says don't.) you really did just take the wrong path, and there's always time to backtrack a bit, or leap around and get in front of the target and start tailing them again.

" Brotherhood made me realise that AC isn't actually a very stealthy game. Getting 100% in soe of the missions was stupid and had to follow a very specific path. I wouldn't go as far as saying it's weird, but not really how it should handle itself. "

I know which bit you're talking about and I agree that that particular mission was a pain, but I don't remember finding any other points in the game where I had the same difficulty with a tail mission, generally they were relatively easy and fun.

Yeah it's way more linear and I don't like that. It's because of getting 100% sync that they make you go in a linear path unlike the last game.

" Edit: I'll accept the idea that I'm doing something wrong, but I can't put a finger on it.   I loved AC2 to death. The controls weren't perfect and getting Ezio to do precision jumps can lead to frustration, but I enjoyed it because I liked climbing builds and stabbing people. No doubt after reading the GB review and other outlets of praise, I saved up enough money to by Brotherhood ASAP.....and I'm not enjoying it.  This is going to be hard for me to explain, but bear with me. Most of the games missions revolve around tailing and killing a target without being detected. Great! I love stealth! The problem is that the game seems very scripted on how you can do this. It seems if I go out of line I have to do it over. One mission had me tail a banker. My first though was to stalk him via the rooftops and chase him down. The buildings dead-end and If I were to jump down, I would get detected and have to start from the checkpoint. The "correct" way of doing it was to hire prostitutes and try to lend in with the crowd.  Then you send in your assassin's to take care of the remaining guards very quickly.  It seems like I have to start over because the game says so. Assassinate a guard the wrong way...automatically detected. I don't mind losing in games because I like to learn from my mistakes, but when I fail to see the mistake I did, I get frustrated.    When the game asks you to be precise and presents a time limit, it gets frustrating. When you get to plan and have freedom in what you do, the game shines. Sadly, this is very rare. There are many other frustrations that are hard for me to describe at the moment. The game also has a hard time communicating with the player at times and the draw distance when running is really bad and many other small problems that get in the way ruin this game for me.       "

You have to keep a safe distant with that one. Yeah it is more linear with the structure of the missions but I never encountered any problems with it

Man, yeah, the Banker assassination sucked. I had no idea there was a cutscene before you could knife him, so I was doing all sorts of unnecessary stuff trying to remove guards so I could get in. At one point, I had actually removed all the guards around him with my sidekick assassins... only to have more spawn right on top of me when I got close enough to make him move to the party.
 
Besides the multiplayer, I'm kinda leaning toward the idea that I liked AC2 better. Brotherhood has tons of missions where if one guard sees you... you have to restart. The reloading really pissed me off (and this isn't Super Meat Boy so it feels like it takes forever). Add on 100% Sync requirements... and stuff gets annoying fast. I remember one mission from AC2 where if guards saw you it was game over. Not a fan of that.

I had to get fairly creative for some of the 100% like shimmying up the side of a building for a good 10 mins so I can go around it. Still, I found the game is usually pretty good as giving you a bunch of different paths you can take as long as you use your head and manage to recognize them. 

As others have said, that particular mission was a pain in the ass, but I don't recall any other missions where I encountered the same level of frustration. 

The 100% synch requirements seemed blatantly unnecessary to me. Its hard enough in any AC game finding all the collectibles, code bits, and exploring secret caverns to get close to 100%, and then to have another layer added on that seems unfair.

" The 100% synch requirements seemed blatantly unnecessary to me. Its hard enough in any AC game finding all the collectibles, code bits, and exploring secret caverns to get close to 100%, and then to have another layer added on that seems unfair. "

I didn't had any troubles and I only restarted to a checkpoint when I was detected or dead.

I'm not usually very patient with games but I guess this one just clicked for me.  I went the 100% route on the first 6 or 7 sequences of the main missions just because I was enjoying playing it that way - it usually just felt more... assassiny?  Which is what I want out of this series.  I never really found it especially difficult or frustrating (the end missions might be IDK- I stopped 100%ing when the story urgency seemed more important), just had to play in a slightly more constrained way rather than just running in and killing everybody (which is fine too if that's how you wanna play it).  Even though each mission felt more restrained this way, I felt like it gave better gameplay variety overall because you couldn't just get through every mission the same way - the pay off was worth it imo.  The last Cristina unlock is at 75% Sync, so there's no reason to bash your head against any particularly frustrating missions if you don't want to.   
 
I thought the '100% Synch' mechanic was a brilliant way of appealing to people that want the game to be a bit more challenging, without alienating the people that just want to hack n slash through it... but I guess not for some people?
 
@President_Barackbar said:

" The 100% synch requirements seemed blatantly unnecessary to me. Its hard enough in any AC game finding all the collectibles, code bits, and exploring secret caverns to get close to 100%, and then to have another layer added on that seems unfair. "

I loved the 100% synch mechanic. It made me play the game in different way's than I normally would. It was a great way of making it more challenging and varied without making the game frustrating.

I don't care about the 100% synch. They focused too much on restricted stealth and too little on platforming, which I think was what killed it for me. I'll play it again in the future. 

" I'm not usually very patient with games but I guess this one just clicked for me.  I went the 100% route on the first 6 or 7 sequences of the main missions just because I was enjoying playing it that way - it usually just felt more... assassiny?  Which is what I want out of this series.  I never really found it especially difficult or frustrating (the end missions might be IDK- I stopped 100%ing when the story urgency seemed more important), just had to play in a slightly more constrained way rather than just running in and killing everybody (which is fine too if that's how you wanna play it).  Even though each mission felt more restrained this way, I felt like it gave better gameplay variety overall because you couldn't just get through every mission the same way - the pay off was worth it imo.  The last Cristina unlock is at 75% Sync, so there's no reason to bash your head against any particularly frustrating missions if you don't want to.   
 
I thought the '100% Synch' mechanic was a brilliant way of appealing to people that want the game to be a bit more challenging, without alienating the people that just want to hack n slash through it... but I guess not for some people?