My favourite of the series was PM: TTYD, which may also be my second favourite game ever. (I didn't have the original PM on the N64.) Everything about it just suited me - the turn based battle, strategy, the story (if cliché) and I still play the game every now and again.
But this thread is about SPM.
Like many others, I disliked SPM at first, primarily because it wasn't TTYD. However, I warmed up to the game later. One of my criticisms about the game is that there is so much text, and a lot of it is pointless. So often, you're given choices (there's even a questionnaire mini-game) and what you do has literally no impact on the end result at all. There are also some parts of the game that feel like a missed opportunity. The game as a whole can basically be summed up as: Walk forward until you hit a roadblock. Flip to 3D. Go around roadblock. Return to 2D. Keep walking forward. Switching partners and Pixls is tedious and they're barely used outside of where you first obtain them.
On the
flipside*, the story is definitely one of the game's strong points, and has one of the best stories in games I've played. It's hard to pin down exactly why this is, but a good example is how the Void grows, and people recognise and comment on it. They know they're doomed yet they continue to urge Mario forward. Nowhere is this done better than World 6. Not many games have characters openly recognise death and their thoughts on it. The variety of worlds is another strong point - they're all different and interesting (though some are still better than others). Put the two together, and you can see the Void consuming heaven and hell - there is no escape; everything really will cease to exist! The graphics are also well done and suit the game, but has the strange side-effect of making some Mario universe characters and items look out of place.
(* Get it? )
Then I got Sticker Star for the 3DS and it disappointed me so much that I haven't even considered Paper Jam...