Genderless Pokemon don't need Ditto to breed, however they cannot reproduce in a way to get you your egg without it. Here is some idea of how they might manage. Since the designation is actually "gender unknown", some of these Pokemon aren't actually genderless, they just have a gender that isn't male or female
- Magnemite reproduce via budding or splitting
- Staryu, Beldum, Rotom, Dhelmise have different genders from male or female, and reproduce in strange ways
- Voltorb, Bronzor, Klink are born from electrical impulses giving strange life to objects
- Ditto are gender fluid/hermaphrodites, and normally reproduce by budding. Assuming they aren't failed clones, that is, though if its both it explains why the population can sustain itself
- Porygon, Baltoy, Golett are artificial in origin and built by man. Only a Ditto can replicate the process, though it's not as difficult and complex as artificial legendaries whom Ditto can't copy
- Lunatone, Solrock, Carbink and Minior are minerals and rocks with strange life. They're silicon-based life forms that could be born from natural forces, a bizarre form of reproduction, or both.
- Manaphy require a royal jelly of sorts to produce more Manaphy, or it will be a Phione
- Cryogonal are born from ice and snow. They create cold environments
Shedinja are a sort of "clone" of Nincada/Ninjask. When a Nincada evolves, the Pokeball accidentally gives life to the shell by copying the personality and information of it. This is why Shedinja's personality and when it meets you, along with its moveset, is identical to Ninjask at their "birth"
Mewtwo isn't just modified because they wanted to make the Pokemon more powerful. The cloning process was imperfect, Mew DNA on its own couldn't sustain itself. There were gaps that needed to be filled with other Pokemon's DNA, which also served as a good excuse to enhance it. Genesect may have also suffered this and some of its cybernetics may be there to sustain the Pokemon's lifeforce, but not as severe since its been several years and research have improved the process.
Porygon's creation was funded by, and involved Team Rocket. You find Porygon the first time at the Game Corner at a steep prince, which Team Rocket owns. The Upgrade is their legal, harmless upgrade. The Dubious Disc, however, was made by Team Rocket explicitly to weaponize the Porygon line. With Team Rocket's decline, the company cancelled production. However they were already produced, and were eventually found again
The reason why Fossil Pokemon are all Rock types is one of two reasons, maybe both in some examples: to fill in gaps in the DNA ala Jurassic Park, and/or because only Rock types are hardy enough for their DNA to survive in fossils so they can be revived...at least by most sciences. Genesect required Team Plasma's additional finances, cybernetics and likely amoral experimentation to bring it back to life.