100% Route
Note: this page was adapted from swordsmankirby's guide. Some strats may be outdated.
The second great RNG boss. Miracle Matter has seven different phases that it changes between randomly. Each pattern can be 1-cycled, but whether or not that's possible can depend on RNG. Furthermore, since you finish 6-3 with lightsaber, getting spark or cutter first can speed up the fight as well. For most of these strategies, I like to stand on the leftmost third of the screen.
Bomb
Since Miracle Matter has 20 sides, the bomb phase only requires two hits, but the timing is arguably the tightest. Despite the randomness in where the orbs shoot and pop, bomb can often be 1-cycled. There are three possible strategies here: single bomb, double bomb, and two spits. When I can inhale one orb near Miracle Matter, I go for two hits using single bomb. The long-lasting hitbox of single bomb allows you to buffer the second hit fairly easily.
If I swallow two orbs near Miracle Matter and no other orbs land near me, I like to use the double bomb powerup once and then throw my powerup away into Miracle Matter. Unlike single bomb, double bomb doesn't have the same lingering hitbox. For some reason, double stars and powerups will pass through Miracle Matter and break right after it exits, so this is another way to anticipate the boss's vulnerability.
Finally, there's spitting two orbs at Miracle Matter, which hopefully covers most other cases. Since you don't have the swallowing animation, the timing is actually more lenient, but the invincibility frames can be misleading. Miracle Matter (and I believe all other bosses, but it's never really relevant elsewhere) stays invulnerable for 0.2 seconds after it stops flashing, so you have to wait a little while before spitting out the second orb.
Cutter
Cutter is perhaps the easiest 1-cycle. The second video shows a faster strat that saves probably around a second. It is possible that MM will spin the other direction, but you can run to the right and swallow a powerup before MM gets to the top of the screen.
Fire
There are essentially three patterns for fire. The easiest pattern is shown in the top-left, and it's faster to swallow the powerup than spit it out three times. One pattern, where MM shoots out four pillars (top-right), cannot be killed in 1-cycle. In the third pattern, MM shoots out two horizontal pillars (bottom). I've found that throwing the powerup for the second hit is the most consistent and safest way of defeating this pattern.
Ice
Ice is fairly straightforward, since the snowball's hitbox is gigantic. Ideally, you want double ice, but this strat can still work with single ice, as shown on the right. The main difference is that single ice's hitbox does not extend vertically past Kirby's hitbox, making the timing a bit tighter.
Needle
Needle is another easy 1-cycle. After swallowing the powerup, jump and use the powerup immediately after. Because of the long invincibility frames, the remaining two hits don't need to be as tight. I like to inch over to the powerup just to save a little bit of time. If the needles spawn counter-clockwise, you should stand on the left side.
Spark
Spark has the lowest probability for a 1-cycle, and I'd say it happens probably around a third of the time. Because of all the RNG, just about all the top runners I've seen will swallow the powerup. MM will try to shoot three lasers at you, so to get them to bounce consistently, I stand all the way to the left and jump over them. The easier pattern to 1-cycle is when the first shot drops as early as possible (left). It's possible to tell when it changes to something swallowable by seeing when it starts to shorten. The second 1-cycle pattern is much tighter, and happens when the third laser drops almost immediately (right). The spark attack's hitbox is pretty large, so you don't need to stand that close to MM to damage it.
Stone
There are a million strats for 1-cycling stone, but the one on the left I've found to be the most consistent and almost the fastest. The stone form follows your position, and I feel like this strat requires the least amount of movement to manipulate MM to the right location.
Other strats include using the stone attack multiple times, or not even using the attack at all and spitting three drops. On the right, I show a strat that uses the stone attack three times. For the second and third one, roll forward in stone form as MM approaches you so that you get pushed to the other side.
Combinations
If you don't 1-cycle a powerup, it is sometimes useful to combine it with the next phase and hope it comes up again. A few of the spark combinations are useful, which is nice because more often than not, you won't 1-cycle spark.
If there are two phases left and the first one isn't 1-cycled, it is almost always better to combine, even if you can't 1-cycle the other phase (e.g. spark to needle). One of my any% records combined spark and bomb at the end.
I'll update this with videos some other time.