I think Superstar Saga is the best because there wasn't much you could do with the formula, or at least nothing they did was particularly spectacular. For me, Paper Jam just felt like "Mario & Luigi & Paper Mario". There wasn't much beyond that they added another character. So, the game play was more or less perfected on the first time out.
Yeah, that's kind of been the biggest problem with this franchise. The first game was amazing for what it was and really played out all of it's gameplay to the fullest. From the combat system, to the overworld puzzles, nothing felt underdeveloped. So when each sequel just keeps reusing many of the same gameplay with no real changes except an extra character, it just got stale.
Of course I feel Bowsers Inside Story was able to still be great because of the Bowser gameplay. Bowsers combat and overworld abilities were unique and offered a fresh take on the gameplay. The weakest parts of that game were the sections where you played as Mario and Luigi, since many were once again rehashing things that Super Star Saga already did better years earlier. Had Bowsers Inside Story just been about Bowser, I feel the game would have been just as good as Super Star Saga. That's why Dream Team was such a massive chore because it's Bowser's Inside Story, without the Bowser sections to freshen things up and the baffling decision to be twice as long.
See, there's a section in Superstar Saga where you have to fight the Koopalings and it is basically one sort of boss fight after another. I found that section got tedious pretty fast and it is part of the reason why I hold back from praising Superstar Saga as much.
Actually this is one of the reasons why Super Star Saga is by far the best. The final section was the perfect way to end the game, using everything learned at that point. Each Koopaling battle had a unique gimmick to it, to really make sure the game got the most out of it's combat system. Every battle increased the intensity until reaching Fawful who had his own unique fight as well. Then you finally take on the Final Boss which is legit hard and a massive spike in difficulty compared to the rest of the game. It's such an epic finale that none of the sequels come close to matching.
It's shows why the sequels all fail to match Super Star Saga because the developers pretty much did everything they could do with the gameplay by the end of that game. None of the sequels feel as polished because they're just throwing stuff at the wall to see what sticks, but not willing to really take any of those idea's to the limit because they don't want to travel too far outside of the comfort zone they created in the first game. Bowser's Inside Story came close, but was still held back by the uninspired Mario & Luigi sections instead of going all in with Bowser. Even Partners in Time which I enjoyed, could have had more potential if it did more with the time travel aspect and made the Baby's gameplay more unique.