All right, ignore the click-baity title and prepare for a long post. But after replaying this game and re-experiencing the storyline after all these years (first played in 05 as a kid and honestly hadn't replayed the full storyline until last summer), I've come to the conclusion that there are many problems with the San Andreas storyline.
These problems didn't appear when it first came out, it only really showed itself when the game was superseded by many other games (GTA IV and GTA V in particular) that it really shows. You have to play GTA IV to understand the biggest issue with San Andreas: the lack of context. Let me give a definition of context:
Context is the background, environment, setting, framework, or surroundings of events or occurrences. Simply, context means circumstances forming a background of an event, idea or statement, in such a way as to enable readers to understand the narrative or a literary piece. It is necessary in writing to provide information, new concepts, and words to develop thoughts.
I'm not going to say that the context within the storyline itself is poorly written, but even then there are issues. But let's dive deeper into the context of GTA: San Andreas and compare it to GTA IV.
In GTA IV, it's made pretty clear of Niko's background and why he decides to leave Serbia for Liberty City; he grows up in Serbia throughout the 70s-90s in relative poverty; his life is relatively normal (there are details like his high school crush, etc) until the 90s, when the Yugoslav wars break out; after this he enters crime in human smuggling in the 2000s, which puts him on the radar for Serbian and European authorities. Part of the reason he needs to leave is for a better life, to reunite with Roman, but also to escape the heat in Serbia. It's made clear why Niko is in Liberty City in the first place.
On the other hand, in GTA: San Andreas, Carl Johnson's background is not nearly as clear. All we know about him is that: his mom was shot and killed, he left for LC in 1988 (the reason itself is never even explained), and he was born in Los Santos in 1969 (heh). That's it. We never really learn too much about his childhood, what inspired him to join the Families (alongside Sweet), why he's such strong friends with Big Smoke and Ryder, or his relationship with his mother. All of this is shrouded in mystery and is really up to the interpretation of the player. You don't really know who Carl really is, just how you interpret him to be.
And when you put it in that frame, the issues with San Andreas' storyline arise even more. For example, why is Frank Tenpenny so corrupt when running CRASH? All you ever know him in the storyline is that he's some asshole who rolls with Fernandez and Pulaski and punishes CJ for no reason other than to torment him and keep his shady schemes going. We never find out who Tenpenny is and how he even joined LSPD, how he got those schemes rolling and how he operates and why he's friends with Fernandez and Pulaski. He sort of just exists as the asshole who keeps you down. That's it. It makes everything feel mysterious and confusing, honestly.
I'm not asking that every character have some uber-detailed backstory. Just some context as to why they act the way they act. The IV equivalent of Tenpenny (Francis McReary) at least had a decent backstory; he was the brothers of McReary and his dislike of the crime life made him join LCPD, and his familiarity with the tactics allowed him to rise in the LCPD. He seems more detailed than Tenpenny honestly.
And I can poke more holes in the San Andreas storyline. Why is Big Smoke targeted and what motivates him to betray GSF? There's some motive (selling drugs and making money off that) but it's never really explored. Ryder's motivations are even less clear and there's a theory that he was shoveled in as a traitor late in the game's development. Why are Cesar and CJ's sister dating? Why is there such a big war between all the four LS gangs in the first place? None of this is ever made particularly clear.
I could even go bigger and question how the environment functions, like why is Los Santos in its present state in 1992 with gang violence, etc? I understand that it's pretty easy to gauge what's going on in the environment by playing the game, but only within the storyline itself. It's not like GTA IV where things are made pretty clear of the history of the environment (they had that whole documentary on GTA IV TV of LC history and character/context clues reveal more about Liberty City). It's never made clear as to what caused Los Santos and the whole state of San Andreas to be what it is in the first place... it can be assumed that the history of San Andreas loosely follows that of real life Western USA/Mexico (from the precolumbian to modern times), and I'm aware of the fact that California was in a very rough state from the 70s to 90s (gang violence, drugs, poverty, etc), but even then, San Andreas is a fictional version of California/Nevada that has its own history that is never really explained. San Andreas just "exists" for the player to roam and play around with, nothing more, nothing else.
Perhaps I'm a bit too hard on this game. Storylines and worldbuilding weren't nearly as detailed or complex for video games in 2004 as they are today, and tbh the first 2 in the III Era have the same issue, but those are smaller so they're not nearly as apparent. For San Andreas, the scope of the game requires all that detail that just seems to be missing. For some reason, San Andreas always seemed "off" to me compared to GTA IV, and I guess I've figured it out: nothing is ever really explained like it is in GTA IV. I'm assuming it's up to the player to create their own history of San Andreas and its characters, but even still, it feels inadequate.
TLDR - the San Andreas storyline is not really that great because the characters and environment arent really explained well compared to GTA IV where Rockstar literally wrote a history for the environment and characters in GTA IV to make it the storyline masterpiece that it was. Not to say that San Andreas is a bad game (its great) and I still like the story; it just leaves a lot of things to be desired.