I can never decide between SA1 and SA2, though some days my mood shifts and when asked I can pick one over the other. There are things I love about SA1 that I was sad to not see carried over to SA2 and there were things in SA2 that I wish were done in SA1.
SA1 had better design. It looked like the obvious next step for the franchise visually, with a bright and colorful aesthetic and while I was not a huge fan of the newly designed characters in the artwork, the in-game models looked great. Sonic, Tails and Knuckles looked great, I loved Eggman's new uniform, though I was sad to see Amy lose the tutu and sneakers. Stages looked cartoony and colorful, enemies were still robotic animals, bosses had very cool designs, E-102 looked like the Eggrobos that I loved from Sonic 3 & Knuckles.
SA1 also had the ability to play through the game as one character at a time, meaning you got to fully experience one character's story and gameplay style. Sure some gameplay styles were not as fun as others, but Amy and Big were not time consuming of difficult and once you completed them they would not appear again. The adventure fields were great fun, I loved just wasting time running about and exploring and sometimes breaking the game.
SA1's story felt like a true expansion on the Genesis originals, with Knuckles' family history and Angel Island playing a critical role. I liked that Chaos was a new enemy, but was tied to an old element of the series. I liked to imagine that he was sitting there inside the Master Emerald whenever I played Sonic & Knuckles.
SA2, meanwhile, had pretty wonky looking character designs. I didn't like how everybody looked a little darker and lanky. I was also thrown by the motion capture they used to animate the characters. It was like the actors over acted their movements, and in turn characters were moving around way too much.
I also thought they moved too far away from the visual designs that made SA1 so great. Things looked more gritty and real. Having said that, the textures were amazing. So sharp and detailed in some parts of the game.
What SA2 has over SA1 is the quality of the Sonic gameplay. Everything felt improved upon, I loved the new moves and the camera wasn't as bad. I was disappointed that we were unable to play as Sonic in the Shadow stages and vice versa in the 1 player campaign, but still the Shadow stages were fun and were essentially more Sonic. Sadly, since they doubled up that meant more shooting stages and more treasure hunting. Sure both were better than the first game, but I felt that there was more emphasis on those gameplay styles and less variety in the game. SA1 had Sonic's speedy platforming, Tails' speedy platforming against the clock, Knuckles' treasure hunting, Big's fishing, Amy's slower platforming and E-102's shooting. But SA2 only had speedy platforming, shooting and treasure hunting.
The Hero and Dark storylines were a novel approach, and were a lot of fun on first playthrough, but lacked the replayability of SA1 I think. I liked going back and replaying as one character in SA1 but rarely returned to replay Hero or Dark because both were much longer and I wasn't always in the mood to play as Knuckles and Tails (or Eggman and Rouge).
I actually really liked the story in SA2. I was less classic leaning than SA1, but exploring Eggman's family was bizarre and kind of cool. I liked how they rolled in the Robotnik name, and the Space Colony ARK was clearly inspired by PSO but with a Sonic twist.
I preferred the overworld map of SA2 when it came to replaying stages, and the Green Hill Zone bonus was very cool (and still is).
SA2 greatly improved on Chao, making it impossible for me to go back and enjoy them in SA1.
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Today, I'm leaning towards SA1, so I'll go with that. But I'd say that SA1 and 2 are like yin and yang. Can't have one without the other and what one does poorly the other improves upon.
Poll