Absolutely.
super paper mario - I love almost all of this game but I have to admit the gameplay is flawed even in my personal opinion. Combat system is brokenly unbalanced, a lot of the level design was dumb, and some other annoyances like the constant menus, the flip meter, and no dash option until Carrie, or Dashell if you want the real deal. Also I feel it would've been nice if some of the unknowns in the plot were better resolved, like Dimentio and Mimi's origins, why Luigi is the perfect host for the Chaos Heart, why did Bonechill escape at the same time as the Void came out, were the memory custscenes Tippi's, or Bleck's or both, if they were Tippi's how was she there during the last two etc.
TTYD - several minor gripes with the battle system like the random buckets that fall from the sky. The villains could have been a bit more interesting. This game also had some level design problems, mainly just too much backtracking. Plus some of the plot stuff is confusing especially at the start when it's not initally well established what on earth is going on
PM64 - gameplay as a whole is kinda outdated, it's annoying to keep having to do these spin dashes to move quickly rather than just hopping on a Yoshi, the timing for action commands feels kinda broken, no superguards, plus I generally find the level design a little too difficult. Graphics are also very much outdated
BIS - graphics, plus as a whole I found the game really cool but just the whole thing didn't really have quite the same atmosphere to me as the first three PMs did.
SSS - graphics, I'm not really a fan of the whole battle system (that applies to BIS too but to a lesser extent), since there's not really any real strategy, just spamming your most powerful attacks and using items to replenish HP and BP when you get low. You can grind to get good and make things easy, but that's honestly just tedious. And if you don't do that, then even just running around into enemies can be really dangerous and constantly annoying and getting in your way, but if you run you lose SO MANY coins, so you're forced to, just to have enough mushrooms to not always die! As for the Cackletta's Soul battle, sure it was a big challenge but honestly not in the right way - it took me like 45 mins because she was just a huge damage sponge who kept throwing new attacks to you that were basically impossible to dodge first time round, essentially forcing me to repeatedly restart, especially with the whole 1HP.
Minecraft - I'd like innate controller support in Java, I feel Java as a whole is kinda laggy especially I can't use shaders with my kind of specs, I'd like for the console minigames to be ported to Bedrock, I'd like the notch apple recipe back, Java 1.9+ updates are cool but tbh I miss the old combat system and have no real way of getting it back, woodland mansions are too sparse, no story or characters. Also being able to easily switch versions in editions other than Java would be nice.
Galaxy (1 & 2) - Luigi postgame in 1, I didn't like, graphics in both could be improved, 1st was generally too easy, green stars were a little tedious in 2, I suppose both could do with more original story and character although 1 was easily my favourite mainline Mario game in this respect as far as the main series goes, especially when it came to Rosalina and her backstory.
3D World - Story and characters, I guess the gameplay as a whole was good but it just doesn't feel like an overall cool experience as Galaxy was because you just didn't feel as in control. Plus 100% in this game is gonna be very tedious - all green stars and stamps, and completing every level another 4 times. Generally this game felt too much like just a generic Mario game.
LIJ2 - hub worlds took a long time to traverse, level designer doesn't have officially supported level sharing of any kind, combat system is way too easy and simple, including vehicular combat. The whole stud system is broken as a lot of the stuff is way too expensive to pay for by conventional means but the moment you get a super bonus minigame it's money no object.
DKCR / 3D - Story and character, 3DS version's graphics and controls, could have done with some more gameplay elements like powerups, a level designer would have been incredible but I guess that's more a thing that'd be suited to a separate game than an addition to an existing game.
MP9 - since getting my new and super awesome mega TV this is the only game I've played on my Wii U... and I have to say I'm dissappointed with how it looks. I hope this isn't going to be the case with all Wii games, but it looks really bad all stretched like that, something I wish would be fixed. Anyway, the gameplay is too luck based, and the things like Boos and Bobombs that would cause you to lose half your stars were so not ok. Also, we all know I'd be ecstatic to have original RPG characters in Mario Party, which sadly isn't something MP9 does.
SMM1 - Lots of bad levels out there, but I guess that's kinda inevitable. I guess it might have been nice to have more customisable 100 Mario challenges - like difficulty is the only filter we had in this game. What about game style, location, or level type? Main thing which could be improved is that lots of things were missing from the original games, such as slopes, an issue hopefully SMM2 will greatly mitigate for me
3D Land - story and character, more original bosses, graphics I guess could be nicer though they weren't at all bad, general theming is much too generic, levels don't have names, maybe make it so the minus button gives you the powerup especially since I can see that being an issue when setting this game up in Citra. Generally I'd like the game to be harder. Thankfully, 3D World answered most of my wishes here.
That's pretty much as far as I'd go with "love" but honourable mention to Super Mario 64 - a game I enjoyed but yeah is a bit outdated and I was never really a fan of the style of level design used by this game or Sunshine.
Wow this took me a while