Though I'm not sure it's one of my favorite games ever, SMRPG still holds high regard in my nostalgia bank. It was one of the first games I owned/played seriously, and I still think it has a unique enough style (traditional JRPG trappings plus Mario, not the other way around) to merit a true-blue sequel. I love the soundtrack (if you haven't downloaded Heavy Troopa is Ready To Launch! yet... well, okay, quite a few of the remixes suck, but there's an equal amount of good ones), I love weird stuff like a cloud-person who thinks he's a tadpole, fighting a living cake (and carrots and artichokes), and anthropomorphized weapons for bosses. I love riding a minecart in quasi-3D and blasting out into a town full of moles. I love the "nostalgia curtain", and I love Mario's ridiculous pantomiming and sound effects in the cutscenes. I love that the first major fight takes place on giant chandeliers, and I think I still get goosebumps whenever I see Mario do his pre-battle "bring it on" animation. Oh, and I love the comparatively badass magic attacks, even if I don't know why everyone gets a card suit symbol.
Also, as an RPG, the game was heavier on plot than any Mario (dare I say Nintendo?) title before, and so there's also a part of me that likes those weird references that raise so many questions about the scope of Mario's world. Mario is apparently famous (people have dolls of him, Peach, and Bowser, or ask him to show off his jumping), Toad references Bruce Lee at one point, and who even knows what the story is behind Geno--the doll or the spirit that inhabits him (I could mention the Link and Samus appearances, but I'm willing to not worry about those for the silly cameo they are). Although I love the Paper Mario and Mario & Luigi series, too, it's for different reasons. Like I said, it unquestionably influenced RPGS from both Nintendo and others (and for having Bowser and Peach playable, Mario games in general), but SMRPG stands alone.
As far as "oddities, grievances, [and] personal beefs" go, I suppose I can think of a few. For one, the prerendering looked great in the game, but doing the art in the same style was... interesting. I'm pretty sure I mentioned this before, but everyone looks like they're made out of painted craft balls, or something (makes sense for Mallow, though). Meanwhile, I don't know if this has anything to do with the art, but it took me a long time to realize what was up with that guy riding Mack, and I'm still not sure what's going on with Belome. Also, I had no idea how music scales worked when I was a kid, so I was hopeless in getting anything out of Tadpole Pond. Also, as a (Square) RPG, it had the requisite weird rare enemy (that cloud thing), bizzare event triggers (talking to that kid over and over until he lets you play the Beetle game, which is apparently for the Game Boy but has a SMW backdrop. Not that that matters.), palette-swaps for stronger enemies, one or two crazy-difficult challenges for an item (guessing what Grate Guy has in his hands, doing some massive amount of Super Jumps), and multiple fake-out bosses and boss phases. Not that any of those things were bad--of course, they returned in future Mario RPGS to great effect.
I'm sure I'll somehow think of more to say. This thread was long overdue!