For my favorite Paper Mario partner, I'd have to say Lady Bow. Sure, she can't really do much against armored targets, but if there are unarmored enemies in your way, Fan Smacks for DAYS. And the ability to avoid tight situations is pretty obvious. Lastly, there's a certain charm to a Boo that won't hesitate to literally smack some sense into those stubborn enough to get in her way.
TTYD partner? That's easy. Mario's greatest ally in any adventure is a Yoshi, and the little Yoshi brings all of the best qualities they have.....and then some. For one thing, he helps Mario get around quickly in true Yoshi fashion. From speeding about in the field to hovering over gaps all while carrying Mario, that's pretty impressive for a newly-hatched Yoshi. His battle prowess is nothing short of glorious. He can use his enemies as ammunition against their allies. He can nail multiple targets with eggs and shrink them in the process. He can call in a stampede to ravage the entire enemy team. What more needs to be said? Have a few BP to spare? Give him a Power Plus P or 2 and watch him REALLY go to town. And like any Yoshi, he has multiple colors(and hairstyles) to choose from, with the red Yoshi being my favorite. I would've picked the white one, but the hairstyle is kinda lame. Red had the coolest hair.
General Guy: The Toy Box was one the most fun areas in any Paper Mario game to date. This place had a lot going for it, cake mixes for those awesome recipes, the defense-breaking Watt, and TONS of mischief-making Shy Guys. I don't think there is a being more versatile than a Shy Guy. Seriously, there's a Guy for any purpose you can think of. But they weren't causing trouble just for the hell of it; they were an actual army. An army led by the stylish and classy General Guy, sporting his badass toy tank. I'd like to think that there are very few bosses in the series that are as likable as him.
Bonetail: No RPG should be without a gauntlet filled with some of the toughest enemies ever. Which is a notable fact of the Pit of 100 Trials, particularly the later levels. Enemies have lots of health, defense and attack power, all of which can put a massive strain on players who aren't adequately prepared. But just when you think you've had enough, you press on into the final chamber which looks pretty empty.....until you realize you're in an oddly familiar cutscene. And the bony big bad makes his appearance. With even more health and attack power than the Shadow Queen, combined with the ability to heal and cause a variety of ailments, any first-timer would most likely be thinking "Well, f**k". I can't really remember the last time I had attained a high level of satisfaction as when I beat Bonetail. The challenge is that it wasn't really the difficulty of the fight(it kinda was hard though, a few times I was unsure that I'd make it)but that he was the final hurdle in a series of already grueling battles. Made for a satisfying finale in my eyes.
About SPM: The shift towards platforming-style gameplay was an odd choice, being that Paper Mario made its name as an RPG. But as far as gameplay goes, SPM is a very solid title in its own right. I mean, it's Classic Mario with a Paper Mario flair, it can't be all bad, right? But the lack of partners is the one truly disturbing change. The Pixls were more like abilities rather than actual partners, but you had to switch them out like partners if you wanted a different ability, most of which should've been permanent abilities as in previous titles.
Hooktail is a she, actually. Just wanted to point that out.