I've been meaning to post my own experience with these guys for some time...
Boss Battles Intense “Strategy” - Pokémon Trainer -
Rock Smash 'em to oblivion.By now, this reliable (and simple to master) route is common knowledge, but it works.
I used Squirtle for the first 5 bosses and Charizard’s side+B and super-armor for the final 5.
I've listed the approximate number of Charizard's side+B needed to defeat a particular boss.
Also included are a few techniques for dealing with
some attacks. CHA=Charizard, SQU=Squirtle.
Boss Name / side+B / Difficulty
+ attacks
Master Hand / x5 / Easy Finger Twist: stay off the stage during its start and Waterfall above it (SQU) to evade it.
Alternative 1 - up+B (CHA) at the right moment to escape with a few scrapes.
Crazy Hand / x5 / Easy Writhing Hand: as he's wildly flailing around, Flamethrow it (CHA).
Petey Piranha / x10 / Easy Cage Swipe: it's only the bottom of the cage that hurts, so attack the head (SQU).
[I tend to focus on the right cage after getting used to fighting Meta Ridley]
Ridley / x6 / Medium Dash: dash to the opposite end and wait until it reappears, then just roll-dodge it.
360 Swoop: unless you're great at air-dodging, this attack will be the only one to deal damage.
Roar: unlike Rayquaza's own, this one hurts if you're too close to its mouth during its start.
Meta Ridley / x6 / Medium Growl and Swoop: this is usually what he starts off with. Rock Smash 2x and air-dodge the "swoop."
Rapid Fire: dash towards the back of the ship and hang onto the edge until it's over.
Triple Fireball: don't try to hit him him during the start (SQU is too weak and CHA is too slow).
[Prepare to air-dodge immediately after you inflict damage and he flies off the screen]
Rayquaza / x10 / Hard Thunder: Take the hit but up+B out of it to lessen the damage (CHA).
Alternative - Pokémon Change, though I seldom resort to doing this against him.
Tail Swipe: wait for him to coil up and a simple air-dodge is all it takes to evade it.
Roar: this is only a scare-tactic. Rock Smash him 2x if possible. (CHA)
Extremespeed: SQU can just crawl under it. Roll-dodging with CHA produces mixed results.
[Note: he does this 3 times if he's at lower health... just a heads-up]
Porky / x8 / V. Hard Laser: Triple jump above it and air-dodge it the first time. Up+B the second time (CHA).
Claw Jab: roll-dodge to the opposite side and commence Rock Smashing 2x.
Float & Zap: dash right into the light cone to activate it and keep rushing past it.
[Also, be careful of any remaining Porky Clone Bombs left on-screen after he's beaten]
Duon / x6 / V. Hard [Blue Side]
Triple Slash: walk towards it and air-dodge once it starts to attack, then retaliate w/ side+B.
Slash Wave: air-dodge and use the last jump to attack it with a side+b before retreating (CHA).
[Pink Side]
Missiles: I take the risk of running them straight into Duon with PKMN Change as a last resort.
Alternative - detonate them using Flamethrower (CHA) and dodge-roll away immediately.
Blue Lasers: if you're grounded, try to sidestep them like Tabuu's Red Rings.
Spin: this usually racks up the damage for me. Try to get out of it with up+B (CHA) if caught.
Switch Sides: jumping over it with up+B (CHA) is necessary, otherwise just air-dodge.
[Note: sometimes he'll do this twice in a row, so jump once after landing just in case he does]
Galleom / x6 / Easy Missile Launcher: if he begins the fight with it, you're in luck. Rock Smashing time.
Tank Form Dash: this usually follows the missile barrage. Land the final hits once he transforms.
[Rock Smash was made for this guy... he's nothing but an overgrown metal target]
Tabuu / x14 / Medium Red Rings of Doom: stand near one of the edges, sidestep-dodging from there is easier to me.
Diamond Saw: I usually take damage here; the initial sweep is simply too fast (CHA).
Eye Lasers: this is your chance to let 'im have it. Try to connect with Rock Smash 4x.
[Don't forget that Charizard has 3 jumps.. make use of them]
I should probably mention that I "choose" Duon as my first opponent. The last one was Crazy Hand.
After 20 attempts or so, you should be able to predict most of their attacks and retaliate.
Your prize: A familiar-looking purple Landmaster for Falco...

Tankmaster?
After a month not playing the game, I finally beat boss battles on Intense...
Just wondering... did you accomplish this using Toon Link? If so, I vigorously applaud your effort.