ME2 wasn't a bad game and it hardly merits being called "an amalgamation of disconnected fanfics". It was a dumbed down and streamlined RPG which relied too much on characters and voiceover. Andromeda and DA:I remind me of a bad fanfiction.
It was a bad RPG, if you can even call it that, and a mediocre cover shooter. ME3 was the game that actually did great in the general direction of gameplay they were going with. It really isn't a stretch to call it a mash of fanfics considering half the game is disconnected stories pandering to fans to get some personal information about their favourite character. That's fan fiction writing.
20 missions are just recruiting and loyalty missions. What are the good ones out of these?
1. Tali's recruitment mission: Great, and actually featured one of two fights on Insanity which required any sort of "strategy". The story part is bogged down by the fact that dark energy plot was not continued.
2. Mordin's Loyalty Mission: Just great overall. The only bad thing I can say about it is no matter what dialogue choice you choose, Sheppard gets all high and mighty about the genophage while Mordin calmly dismantles anything Shepard is crying about.
3. Legion's Loyalty Mission: The only impactful choice in the entire game. Unfortunately a little soured on that because of the "i wanna be a boy" direction they took with the Geth, some of the only good sci-fi writing in the entire franchise.
So out of all the missions, these are the only one's that connect to the actual story of Mass Effect in any way and 2 of them are broken story wise because of the direction the series took. That leaves 17 missions of self contained personal stories that have literally no connection to anything, and are essentially just pandering to fans, that seems like fan fiction writing to me. Don't get me started on the 5 "main story" missions.
As for the "good game" part, the discussion about gameplay is a whole other beast.
ME3 retcon of the Reapers and introduction of Deus ex machina killed the plot
The retcon of the Reapers already happened in ME2.