Ahh, this will be cathartic.
First off the storyline. It starts out pretty strongly, and I remember being amazed at the events that transpired in "The Green Sabre". But after that, the story loses some focus. At first the protagonists seem pretty focused on freeing Sweet and getting back to Los Santos, but eventually it feels like they forget about it. It feels like the writers played their best card too early.
I also don't like numerous plot threads that never come to fruition. We never get to directly confront the Ballas who killed CJ's mother. "The Introduction" video seems to imply that it was just some random soldiers, not anyone important, but it feels really weird to not have a confrontation with them. I'm sure some people enjoy speculating on what happened and like the ambiguity, but I really would've preferred to find out exactly what happened to Brian. I think it would've provided key insight into the motives of both Carl and Sweet. I'm also disappointed that we never get to find out what the Green Goo was.
There was probably no way around this, given how big the map is, but one of the things I missed most from the previous games was having a central base of operations. You had one hide out per island in III, and the Ocean view hotel and Mansion in VC. You don't get that in SA, and it's less conveniant. And given how many vehicles and pick ups spawned in the Vercetti Estate, I really wish I could've had something similar in SA.
The collectables are annoying in this game. In previous games you get weapon pick ups at certain intervals, but in SA you need to collect all of the pick ups before you get anything for them. It's very hard to do without a guide, and even with a guide it can take hours. The tags are kind of unfair, because how hard they are to see depends on your brightness, the weather and the time of the day. And yet, after you spray one over, the Grove Street tag is always perfectly visible no matter what, which seems pretty unfair.
I hate the Badlands section because of how far apart the mission objectives are. I really don't know why they thought it was a good idea to make the players travel so damn far, and plotting a good route through the area isn't easy.
While III and VC had missions that are incredibly frustrating, SA is worse than both of them combined. Wrong Side of the Tracks, Zero's missions, Flight School...hell, at least The Driver was optional. Challenge is one thing, but most of these missions are difficult because they're badly designed.
Speaking of frustrating missions, I wish the schools were actually more like schools. They should have told you how to do the manuevers, not just tell you. To this day, I have trouble with the P.I.T Manuever because the game doesn't do a good job of telling you how to pull one off. Also, driving school should not have been a prequisite for the Steal Cars strand. Remember what I said about the characters forgetting about Los Santos? Well, that mission strand has them discussing it. Some of the most relevant character interaction happens in optional missions.
While separation between the gameplay and the story is difficult to avoid, and practically impossible for a series like GTA, I think SA was worse about it than it needed to be. Carl might complain about needing money no matter how much you have. This is something that was easy to avoid; they simply shouldn't have had Carl needing money as a plot point. The more you hate Tenpenny, the harder it is to ignore the fact that you can kill every cop in San Andreas except him. It makes sense when Sweet's in jail, less so before that point. A lot of games might vary the dialogue based on what you do as little easter eggs. GTAV had a lot of that. I don't think how common it was during SA's era, but I wish the game had more of it. I was disappointed to find out that the other characters always criticize CJ's driving no matter how careful you are.
The property assests are much less satisfying than they were in GTAVC. The majority of them don't even have a story behind them. Going by the story, all CJ has by the end of the game is a chop shop, an electronics shop, an airfield, and a stake in a casino. Kind of disappointing for a guy who went on a crime spree across the whole state.
The stats definitely could've been better. Having separate stats for most of the weapons seemed excessive, as does having separate stats for cars and motercycles. In particular, you have to really bust your ass to get your driving stat up. Without doing a lot of the side activities, you can go through the whole game and maybe get it halfway full.
Forcing CJ to eat was a bad idea. It's not much of a problem if you just go from mission to mission, but if you spend a lot of time exploring, you're forced to drop out or risk losing health. It's not fun.
CJ...a popular protagonist, but also probably one of the most divisive. I like him overall, but there were some problems with how he was written. It seemed like they wanted him to be more sympathetic, portraying him as someone who only killed people who were messing with him or his family, or being forced to kill by people like Tenpenny and Toreno. But CJ wreaks plenty of his own havoc through the story. He murders several construction workers for being impolite to his sister, the Heist stand requires him to murder people who had done nothing aside from being in his way, and his ruins Mad Dogg's life just for OG Loc's sake. And it's pretty clear he has no faith in Loc's ability to become a star, so what was in it for him? It seems like some of the missions were written by someone who wanted CJ to come across well, and others who written by someone who just wanted to write GTA missions regardless of characterization.
Following on that, I read a review that expressed disappointment that the game didn't focus more on CJ's warring desire to help his family and his desire to go straight. At the beginning of the game, CJ tells Tenpenny that he's legit now. But "The Introduction" has him hijacking someone, and shows that he was stealing cars for Joey Leone. Did the writers change their minds, or was CJ lying when he said he wasn't committing crimes? An interesting moment is in Los Sepulchros, where Sweet wants to hit the Ballas at a funeral, which CJ is clearly uncomfortable with. That could've made a good plot. CJ wanting to help Sweet, but feeling that he's going too far and becoming no better than the Ballas.
I seriously hate how some missions automatically saddle you with a certain weapon, even if you were carrying a better version of it. Hope you don't feel like using the Desert Eagle during Las Venturas, because it'll be replaced by pistols several times. It might be easy to ignore if you got your original weapon back afterwards, but as it is the game punishes you for being diligent.
Some of the changes to the gameplay are annoying. They changed the radio station button from the shoulder button to the D-pad. So now I have to take my hand off the joystick if I want to change the radio station. They thought this was a good idea, why? The camera also works against you too much. It hangs too low, which can make races more difficult than they should be because you can't properly see in front of you. The aiming system is a big step up, but some things needed to be changed. Unlike most games, CJ won't aim where the camera is turned, but where he's facing. Switching targets won't prioritize armed targets over unarmed ones, so you better hope there aren't many peds around during a gun fight.
I love the Gang War system, but some of the sections are too freaking small. Even worse is that you have to kill gang members on the square to trigger a gang war. On the smallest strips, it can be very difficult to make enough gang members spawn, and Rockstar really should've programmed them to spawn more frequently when gang wars are active. Near the hospital, they may end up spawning so far away that they can't get to you and you can't get to them without deactivating the fight.
Smoke's courier missions are annoying. They always start out very far from your location, so going after them is usually more of a hassle than it's worth. But the worst part is that I'm a bit of a perfectionist. I feel like if I don't do them, then I'm letting Big Smoke get away with what he's doing. But then again, even if you do ace all of the courier missions, it doesn't seem to affect Big Smoke's wealth at all.
San Andreas is a great game overall, but I feel like it's a game that tried to do a little too much. Out of all the GTA games I've played, I think SA is the one that I feel needs the most refinement. Not additions, refinement.