Mario - I can see the logic behind the Mario Finale: as the "average" character in Smash, it makes sense for him to have an "average" Final Smash, a giant fiery blast with no other quirks. However, though Mario does use a lot of fire in his various games, it's not one of his major defining aspects.
What would I suggest? Retro Starman. Mario grabs a Starman, which doubles his size and makes him 8-bit. He can then run around and damage other players by running into them, or jump on them to deal a lot more damage. It lasts for 10 seconds, same as in the original.
Luigi - The developers likely developed Negative Zone as a "generic" Final Smash on the side, then decided to give it to Luigi for no apparent reason. It just doesn't make sense any other way (as both ZA WARUDO and acid trips are not very Luigi-like)
What would I suggest? Well, there's always the Poltergust. It could have a huge suction effect, and if he could suck the other players into the vacuum, it would deal massive (upwards of 70%) damage. Or, he could transform into the final boss from Super Paper Mario, which, while still WTF, makes a whole lot more sense than a random acid trip.
Peach - Her dancing is so terrible, it bores her opponents into sleep. Then she makes peaches appear. That's really subtle, Sakurai.
What would I suggest? Well, Vibes from Super Princess Peach would work, most likely Anger (which sets her aflame). A more inspired one would be giving her a magic wand from Super Mario Bros. 3 - her normal attacks would fire energy rings in a given direction, while her B attacks would fire more literal rings that bounce around the stage (Wendy Koopa's attack).
Bowser - Giga Bowser was a no-brainer for a Final Smash, but it's still somewhat lacking. If Giga Bowser had a lot more attack power, it'd be better. But a more canon one would be giving Bowser his Clown Car, and letting him fly around on that while dropping physics-defying bowling balls and whatnot.
Another alternative I thought of was teleporting all of the characters to a bridge reminiscent of the boss battles in the original Super Mario Bros. Bowser would become invincible, but if any of the characters hit the axe on the other side, everyone else would fall in the lava and take damage (Bowser would only take half).
DK - I have no problem with the FS itself, but it could be a bit stronger.
Diddy - It's a bit uninspiring to just put 2 of his B moves together and call that an FS. I haven't played DK64, but if we go by DKC2 and 3, he could call up an animal buddy, tag-team with Dixie, use arrow barrels to shoot all over the place, etc.
Yoshi - I was actually predicting something like this, though only with limited flight and yellow shell powers (powerful quakes when landing on the ground). Other FSs that could work: calling in a horde of Yoshis (ala Melee's intro video), replacing his neutral B with spitting watermelon seeds, something involving fruit, or calling in Giga Baby Bowser (final boss of Yoshi's Island).
Wario - I was hoping for one of his Wario Land powers, but Wario-Man works much better. No problems.
The entire Zelda cast is okay, though Link and Tlink's could be something a bit more specific to their games (Fused Shadow Midna, flooding Hyrule), seeing as these two Links specifically represent Wind Waker and Twilight Princess.
Samus - despite being non-canon, the Zero Laser works quite well for her. The Hyper Beam/Phazon Beam would also work, as does just destroying the planet the stage is on, but the latter is a tad bit broken. I'm disappointed Zamus didn't actually use the Crystal Flash, just a cheap imitation of it.
Pit - after having played Kid Icarus after he was announced, I don't know much about him, but he could have also used his upgraded form present in the final level, though it would be pretty similar to Yoshi's. In fact, Palutena's Army would probably be what Yoshi's Horde of Yoshis Final Smash would be like... hmm.
Ice Climbers - Frankly, there's not much to mine from the original Ice Climber, so calling in a giant iceberg works. It's too bad that there's not more stage-modifying FSes, though.
ROB - His FS sucks. Period. Sure, he's invincible, but eye lasers are played out.
But again, there's not much to Gyromite and Stack-Up to get an FS from. Detonating a Subspace Bomb might work, as long as getting drawn into Subspace somehow worked to ROB's advantage, but if you unlocked him without playing through SSE, that would be a bit of a spoiler.
Kirby - I was predicting Crash or Mike, though both would be a bit overpowered. Cook works perfectly, as it sums up Kirby in a nutshell - he likes to eat things.
Meta Knight - Galaxia Darkness works to a point for MK, as he requires precision and good timing to play well. But he had other potential FSes as well - calling in the Meta-Knights as assist trophy-like fighters, air raid by the Halberd, or unlimited flight for 20 seconds. But again, his current FS works for him.
D3 - Other than the anime, Waddle Dees have never really been in the service of Dedede. But, like MK, Waddle Dee Army does work for Dedede, as he's a fat, lazy king who employs others to fight for him. And there's not much else he could do, other than being possessed by Dark Matter and getting a different moveset.
Olimar - Having never really played the Pikmin games, I can't really speak for End of Day. A Pikmin army would be awesome but redundant, and there's not much else he could do.
Fox/Falco/Wolf - The less said about Landmasters, the better. But Falco and Wolf could've easily got other methods of transportation (Arwing/Wolfen).
Captain Falcon - Blue Falcon is what I expected, though the weird cinematic roadkill-maker was a bit weird. Again, from the source material, there's not much more he could have, other than a barrage of F-Zero racers like that one Event Match in Melee.
What I did consider, though, was a remote-control Falcon Flyer, controlled by the taunt buttons. It would be something like the platform in Big Blue, but with lasers. And the Galaxy Falcon Punch would be awesome, but... no. Let's not go there.
Pikachu - A massive thunderstorm would've worked, but Volt Tackle, being his signature move, is just as effective. I've also heard that it's a reference to an old Genesis game, which doesn't really make sense, but eh. Pikachu has a bunch of other potential Final Smashes, but none of them really work as well.
Pokemon Trainer - It was either Triple Finish or a legendary Pokemon, and Triple Finish is probably better. The "It's super effective!" box is unnecessary, and should've been removed.
Lucario - KAME-HAME-HA! Lucario himself is a thinly veiled reference to Dragon Ball Z, so it makes sense that he has a finisher clearly inspired by Goku's trademark move. Aura Storm works for him, though it could've easily been called Hyper Beam or even Flash Cannon.
If we go by the games, Lucario could've also used Giga Impact or Close Combat, both powerful physical moves, or a "buff" attack like Swords Dance or Iron Defense, which would increase his attack power or weight, respectively. Maybe even Ancientpower, which would do meager damage if it hit but would make Lucario a lot stronger... hmm. But they made the right choice with Aura Storm, I think.
Jigglypuff - Seeing as how Peach stole an AoE Sing (and how does that work, exactly?), Jigglypuff... gets to inflate. While the Gigglypuff glitch is fun and all, it's not all that special.
Hyper Voice, which would be something like DK's, could've been a suitable replacement. As would Metronome, which was suggested earlier in this thread, though it's usually seen as Clefairy's signature attack (I can't even remember if Clefairy is in a Pokeball this time around). And, if they were really desperate, Double-Edge, which would instantly KO an enemy no matter what but deal significant damage to Jiggs. But Puff Up?
Marth - Having never played Fire Emblem 1 or 3, I'm not really sure what else Marth could use as an FS, but, like Meta Knight, a hard-hitting precision attack seems to be in the spirit of the character. But why does it KO instantly? Marth shouldn't have that kind of power. If it was a bit weaker, it'd be perfect.
Ike - Great Aether makes my head hurt. It's pretty much a clone of Triforce Slash, which is itself used twice, but with TEH PHIRE! Having played PoR and RD, Ike had a few other options: calling in the Greil Mercenaries up for a raid would be the top one, as would buffing his regular attacks with sword beams (seeing as the Ragnell was capable of such). Heck, even calling in Roy for some assistance would've been cool to see. But no, TEH PHIRE is supposed to amuse us.
Ness/Lucas - Seeing as how their other B moves are borrowed, PK Starstorm, an attack learned by their teammates (Poo and Kumatora, respectively) is the cherry on top of a sundae of unoriginality. However, PK Rockin' and PK Love are both pretty abstract animations, and would be difficult to convey as Final Smashes by throwing lights and sparks all over the place, so I can see how Starstorm works better in that respect.
Mr. Game & Watch - I think the only reason that they made the Octopus his FS is because of the ladies in the roster. In fact, that might be why there's so few ladies in the roster in the first place...
But having never touched a Game and Watch, I can't say much. From the Flat Zone stages, it doesn't look like there's much in the way of FS-worthy material in it. There's always transforming into Duon, but the less I mention of that, the better.
Snake - Snake's supposed to be a spy, not a crazy grenade-launching maniac. But it'd be pretty difficult to do anything spy-like (like slitting their throats) without it being too graphic for all of the kiddies. Hopping into a Metal Gear would've been cool, but runs into the same problems. I've only played parts of the Metal Gear games, so I can't say much else.
Sonic - Super Sonic is too strong, but it's a perfect FS for Sonic. Nuff said.