I'm more partial to Paper Mario myself. Mario & Luigi games have some very nice and well-thought-out game mechanics, and the interactions between Mario and Luigi are funny and adorable. I've always been a bit more drawn to Paper Mario's simplicity and the partner system (I love goombas and koopa troopas, so games where you get to add them to your team appeal to me). I guess I also prefer the overall world-design in Paper Mario, though M&L do this nicely as well (Beanbean Kingdom is a very interesting location).
Though making a concrete decision is a bit tough since my interest lies mostly with the earlier titles in both series, and completely drops off at some point. So if I need to look at the entirety of both, the question becomes "Which series shits the bed the least after a point?". I think Mario & Luigi's annoying fascination with clinging to Starlow and wasted potential post BIS wins over the catastrophic failure that is Paper Mario post TTYD.
Lastly, Paper Mario: The Thousand-Year Door happens to be my favorite Mario game period, main series included. That's probably the biggest point for me. So overall my personal score is 2-1 for Paper Mario.
The first 3 in each series are all great but I'll give the first game to M&L, second and third to PM. After that, M&L wins every time since Paper Mario decided it would be a fantastic idea to ditch having an interesting story and developing new characters (things I've always considered defining features of the RPGs) in favor of "let's think of cute paper effects and base our game around them, nah it's fine without a story or characters just use i dunno some toads"
Though, Paper Mario does come close to being on top again with Color Splash vs. Paper Jam, but that's more due to Paper Jam being the only M&L to do the Sticker Star thing (and CS at least being an improvement over Sticker Star) but I still don't know which one I dislike more.
Also I'm sure most people who know me know this but since it's a point of controversy I'd just like to make it clear that I'm in the "SPM was good" boat. I really don't find it comparable to what the series became starting with SS, at all.
When I say catastrophic failure, I'm referring to Sticker Star. I agree that SPM and Sticker Star are not on the same level of quality; Sticker Star actually makes me kind of angry, whereas I think SPM was just kind of lame and disappointing. I only specified "post TTYD" because that's where my personal drop-off point is and I stop having a good time with the series.
M&L is better as an RPG series, but PM is better with innovation and uniqueness. I adore both series, though, and I've thoroughly enjoyed every game I've played from both series, with Dream Team being my favorite game of all time.
There's only one Mario RPG that I didn't enjoy too much, but it's the first one on SNES, so I guess it's a good thing that its successors were such great improvements.
I have played all Mario & Luigi games, but only played Super Paper Mario for the Paper Mario series. And there is a reason for this too. And it is that the Mario & Luigi games have been playable on a handheld. As for SPM, it is on the once popular Wii and the other Paper Mario games are 64, GCN, Wii U (home consoles). Sticker Star is the only one that is a handheld, but after looking at the pages and seeing the ratings, it is considered the worst of the Paper Mario games. Anyways. What makes a great game is a story. However, gameplay also plays a role in this too. Minion Quest: The Search for Bowser, the mode in the remake of Superstar Saga, had a good story to it. But the gameplay isn't something that makes me want to play it. In any case, the Mario & Luigi series has always had the same good gameplay mechanics and introduced others after the first game. SPM is a platformer with RPG mechanics and it is not completely fair to compare it to the Mario & Luigi series or early Paper Mario series in mechanics. So, I am on the SPM is a great game to play side of that debate. But, I haven't played either of the first two games. However, I have watched people play PM and saw what events happened in it, but I couldn't completely understand what's going on since it was in Japanese due to it being a speed run. But then again, I have also seen someone's videos of both Paper Mario's glitches and details (though they mainly have/had focused on the 1 one).
So in conclusion: Both are good series and I like M&L better, but that may be due to me playing all of them.
I really enjoyed Paper Mario 1 and 2, but never really cared for Super Paper Mario, and I haven't tried Sticker Star or Color Splash so I can't say anything on those.
I really enjoyed Superstar Saga and Partners in Time, thought Bowser's Inside story was good, and thought Dream Team was okay, I'm currently playing through Paper Jam and it seems to be good enough so far.
So out of the games I've finished, that's 3 M&L games (Probably will be 4) that I thought were good, and 2 Paper Mario games I thought were good. The first two games in both series are my top 4 favorites in the entire Mario RPG series, which can switch spots depending on how I feel.
(I also thought Super Mario RPG was good, but that's in its own category).
All of the above. Mario and Luigi would probably beat Paper Mario by himself in a swimming competition though.
I've always preferred the Mario and Luigi games for several reasons. Luigi gets to co-star with Mario probably for the first time since the original Mario Bros. Practically every other game, Luigi is absent or you use him instead of Mario. This is a good setup that allows more extensive character interactions with each other, and yeah, the game does deliver on it and appears to be even more on that dynamic in Dream Team (though I feel it's pretty significant in Partners in Time too). Paper Mario falls short here. There's just so much more you can do with Mario and Luigi compared to Mario and an underbaked partner that eventually gets replaced by other partners or loses most of its character once the chapter the partner is relevant in ends. I also feel Mario in Mario & Luigi is more involved in what's going on there rather than just staring at what others are doing, but Mario & Luigi isn't immune to it either, because of those accompanying annoying characters like Starlow.
I also prefer Mario & Luigi's art style too. I have a preference for more on-model depictions of Mario and friends. I do like a lot how Paper Mario is depicted (more than years ago but I think this has to do with how I used a Paper Mario over Olimar mod as well as using Paper Mario character in MUGEN), don't get me wrong. I just like the formed legs, the eyebrows, the jet-black pupils, and the expressive faces Mario makes. Bowser looks less puffy as he does in Paper Mario, Peach has prettier eyes, Dry Bones, Boo, and Hammer Bro. look less strange by being closer model to the contemporary designs) (not this weird ass Dry Bones human skull from Super Mario World, not Boo's weird upper lip from the Yoshi's Island games, not these weird "Koopa wearing gear" of Hammer. Bro.). Some people do like the diversion from the contemporaries because they add a degree of weirdness and helps make a game appear more unique, and that's fine, though! I just prefer more subtle arrangements like the black irises or the slightly lankier proportions of Mario in Mario & Luigi Dream Team and beyond.
I do like that Mario & Luigi is built upon having existing characters getting new roles. The first game, as I said, is about Luigi actually simultaneously being with Mario and being able to do cartoon mishaps to each other to advance to new locations and beat enemies. But the second game gives us a rare starring role to Baby Mario and Baby Luigi. The third game also gives us yet a new co-starring role with Bowser, which is the closest we got to a Bowser game in the entire franchise. The fourth game didn't really do anything like the first three, and it was disappointing because it seemed to be a good time to give roles to Waluigi and Wario, especially given with that they did to Baby Mario, Baby Luigi. But in the fifth game, we got the Mario & Luigi world and the Paper world clashing, and it led to ridiculous and entertaining scenarios. Maybe it fell short in giving us both elements from those series, but it could've went wrong very easily and I still think with what we got was super interesting and pulled off pretty well. Paper Mario is capable of pulling off neat story lines, but they seem to do best when they're classic and straightforward, and I wasn't really pulled into any Paper Mario's story set-up as I am to Mario & Luigi. Mario & Luigi just seems to be better at using existing characters than Paper Mario, as Paper Mario marginalized Bowser well after the first game (to be fair, Mario & Luigi Superstar Saga didn't treat Bowser all that well), Paper Luigi just seems to be "there" and has a weird personality clash with the rest of the series, and there's not much other existing characters like Toadsworth, Nabbit, E. Gadd that Paper Mario uses that Mario & Luigi doesn't, though I have to give credit, they did use Piantas. Peach might be the only character that's better than the Mario & Luigi counterpart
The one thing that Mario & Luigi suffers from is that they have an ally that is, well, insufferable: Starlow. I don't know what the developers see in her, but I don't like her and she's wholly unnecessary, as we've seen from how people played the Superstar Saga remake and remarked how "refreshing" it is to feel that Mario and Luigi are really the ones in charge. Mario & Luigi also seems to rely on gimmicks a little too much, which does negatively affect the experience; Bowser's Inside Story has egregious touch screen minigames, Dream Team has the atrocious broken gyro controls that are *almost* as bad as Quick Time Events). Mario & Luigi also never took the opportunity to develop Firebrand and Thunderhand, which is very disappointing because electric and fire elements certainly add more to the mix of dealing with enemies.
I didn't really go into the gameplay sort of things because, to my embarrassment, I haven't played either games extensively though I did watch my sister and brother play those games, but I don't have much of a preference. I like Paper Mario's elegance in how damage is dealt and given. Mario & Luigi has a more traditional system of SP that lets me pull off flashy moves, but I do like their method of relying on cues to try avoiding damage.