I didn't say plot. I said concept.
Mario wouldn't work well if you changed some of the aspects. While Mario is very trippy, it follows a lot of conventions throughout the game. And, this is far more important as games get more and more complex.
Try doing Mario 64 without any direction.
Look at the name, Shoot Em Up. What are you going to do in this game? Shoot things, likely lots of things. Now, lets make the characters a banana, not even really a flying one, just a banana, then have cherries and keys fall towards it and give the player no direction.
What must he do?
Now make it so his life goes down with each hit from the cherry, but his score goes up, and if he shoots one. his score stays the same and his health goes up, but if shoot a key, your score goes up and if you get hit by it, you lose health..
Then in level ten, have a boss battle, where the only way to win is to do nothing, move at all from where the game puts you, and you will be shot and killed in 1 hit.
Then at level 20, add in bombs that heal you.
And finally, at level 50, (this game won't let you save either), add in random lightning bolts, and if you get hit with one your health goes up, then 30 seconds later, you lose 50% of your health per bolt.
Understand? A game without a useable concept is frustrating, not fun, and can be downright unplayable.
Now, preface the new levels with an explaination of what is to come, give the player a verbal puzzle to figger out the boss, and change the cherries into bricks of gold, the banana into a space ship, the keys into other space ships, the lightning into a sticky energy bomb that restores your energy before exploding, and the bombs that heal into energy absorbed by your ship's shields.
Now the game makes more sense, it might be unbalanced, but it is at least playable.
Mario is random and goofy, but new additions follow a logic and can be figured out by looking at them. you learn right away about turtle shells and how they work, when you come across them in the future, as hard beetles or otherwise, you learn how to deal with them. You aren't thrown any curve balls later on in the game, because everything makes sense.
Typically, puzzles lack a good metaphor, they have one tacked onto it sometimes, but rarely use it to drive the puzzles.
There are rare examples tho. Such as The Adventures of Lolo. Where a puzzle game has a strong well thought out metaphor to drive the game.
Lolo is an incredible game because of this. Again... there isn't really a plot. there is, but it is shallow. Your girl's been captured, climb the tower and save her. When you get to the top, wow, you saved her.
It is basically just 100 floors of puzzles some of which are action puzzles.
But you can ruin the metaphor and over complicate the game.
http://www.newgrounds.com/portal/view/314164This is a clone of Lolo without as good a metaphor, different zones too. It begins to wear on you, and were it not for some design choices that make the trial and error aspect at least not kill the play, the game wouldn't be very good at all.
I played through many levels of Lolo without dying, even when there were new enemies to play against, planing it all out from the first moments and remembering what the other enemies do, gets you through it. And often the game introduces a new foe with a simple puzzle using the foe, so you don't have to contend with a lot of other variables.
Match 3 games are hard to put a good metaphor on. Mainly because they are so simple they don't need them. But they don't have to be that simple. Paint numbers on them, have the player be able to match with 3 of a kind or a straight 123 or 765. For that matter, put card faces on the tiles and ask the player to build card hands, 5 or 3. Ace Ace Ace, Ace King Queen, Heart, Heart, Heart.
These metaphors add complexity to the match 3 without making them harder, or requireing you to learn anything new.
I don't know if anyone has ever done those, seems like they should have, since they are such good ideas.
But that is the thing about puzzle designers. They don't always think like that. Just like the RPG designers don't make tactical RPGs where the location you stand in relation to your party can effect the game. I'd like to see a spell that projects your party's location and direction faced out a square or 2, and attacks all those spaces. Or other situations. Or otherwise infusing more of the puzzle designers ability to make puzzles. Since RPGs come down to statisticly driven puzzles, where you know fire beats water and a very powerful warrior might be put to sleep to take care of them. There are mental puzzles, and could be built apon with the right minds.
The amount of RPGs that just tack on a FF style RPG system is staggering. Without changing it at all really. Same elementals, and status ailments with new names. Sometimes not even new names.