I've played every game except for Superstar Saga and Paper Jam. My favourite is Partners in Time(TM), mainly because of the memories and the darker atmosphere. I also enjoyed BiS, but I had an english rom during elementary school, so I didn't understand the story, lol.
Superstar Saga is my favourite Mario & Luigi game, be it just because of Nostalgia, the Artstyle and lovable characters such as the Popple & Rookie duo which you encounter throughout the game.
My second-favourite in the series is Dream Team. Great music, story, graphics, all that jazz. I especially liked how more elaborate attacks and the options to counter them were. My only gripe with it is that often times areas take a bit too long. There's a lot of needless stretching in this game to make it longer. The 30+ hours of gameplay can be summarised in 1. finding the dream stone, 2. getting the zeekeeper 3. defeating bowser. Something which throws the player off-track like when they get stranded in Superstar Saga would've been a nice touch, in my opinion.
Third-favourite has to be Partners in Time. The area is beautiful and I love time-travel. It's also really dark for a Mario game. Maybe if I replay this one day it'll actually rise beyond Dream Team in this list.
Least favourite of the ones I've played is Bowser's Inside Story. To me, it got really repetitive after a while. Especially as all the areas you visit are either Grassland or Intestines.
I have had no chance to play Paper Jam yet, but I've spoiled myself a bit about it, and the only thing I moderately like about it is the main battle theme. Nothing really appeals to me, and to me this seems like a crossover of Sticker Star and Dream Team, which is... why not any of the other Paper Mario games?! Sticker Star had barely anything innovative, and I feel like that carried over into Paper Jam.
Currently replaying DT and I'll hopefully finish it before I get PJ for Christmas.
I didn't remember that game being too great (I actually never beat it), but replaying it now, I'm really enjoying it. I especially like the dream areas and how the enemies there are reflections of real-world enemies and things.
My favorite M&L is probably either SS or DT, with BiS after them and then PiT. I haven't really played PiT in ages though, so maybe I should do that.
My favorite so far is Superstar Saga, with Bowser's Inside Story being a close second. Right now Partners In Time is last, I've yet to play enough of Dream Team to have an opinion on it. I havent played Paper Jam yet.
Mario & Luigi is a fun, RPG Nintendo series that has had five moderately to incredibly well recieved games. Superstar Saga, the first in the series, is commonly cited among the best games for its system, and the accolades have continued since with Partners in Time, Bowser's Inside Story, Dream Team, and now Paper Jam.
Paper Jam came out a few weeks ago in Japan, and the game has been recieving mixed-to-good reviews. The main gimmick is that Paper Mario's universe has spilled into the regular Mario universe, so he teams up with the brothers to stop evil and yadda yadda yadda.
For those unfamiliar or rusty with the series, each installment since the first features a main player character gimmick or trait. Here's a summary of the playables for each game.
Mario & Luigi: Superstar Saga- Mario and Luigi are controlled with the Gameboy's A+B buttons. At many spots in the adventure, the two must separate and control individually.
Mario & Luigi: Partners in Time- Mario, Luigi, Baby Mario, and Baby Luigi are controlled with the DS's ABX+Y buttons. The babies separate from the adults in many situations.
Mario & Luigi: Bowser's Inside Story- Mario, Luigi, and Bowser are controlled with the DS's ABX+Y buttons. Bowser and the brothers are separate for a lot of the game.
Mario & Luigi: Dream Team- Mario and Luigi are controlled with the 3DS's A+B buttons, and sometimes control the personification of Luigi's sleeping conciousness with the touchscreen.
Mario & Luigi: Paper Jam- Mario, Luigi, and Paper Mario are controlled with the AB+Y buttons.
Additionally, each adventure takes place in some unique/modified setting with its own enemies.
Mario & Luigi: Superstar Saga- Beanbean Kingdom with bean/laughter themed enemies/places
Mario & Luigi: Partners in Time- Mushroom Kingdom past with Shroob themed enemies/places
Mario & Luigi: Bowser's Inside Story- Inside Bowser with body themed enemies/places
Mario & Luigi: Dream Team- P'illo Island with dream/sleep themed enemies/places
Mario & Luigi: Paper Jam- Mushroom Kingdom (paper invaded), with paper enemies
So, what do you think the next move for the series is? We have a clear pattern of new protagonists and locations that aren't normally featured, so there's plenty of options! I have a few personal ideas.
Mario & Luigi: Pretty in Pink- The Bros. team up with Princess peach in some new location. Like the Beef Kingdom.
Mario & Luigi: Extended Family- In an unprecedented party of four (IDK how it'd work, most likely only three of them), Wario and Waluigi join the Brothers.
Mario & Luigi: Egg-cellent Adventure- YOSHI FOR THE WIN
I'm hoping that I'll be able to get Paper Jam soon, since it mixes two Nintendo RPGs that I like a lot. Although from what I've seen, it doesn't look like there's Paper Luigi in the party, and that's a little disappointing. But oh well.