There are a plethora of factors that go into price differences, anonymous, and it certainly doesn’t help that there isn’t really a standard for such. (There really should be, but unfortunately, the Pokémon Association thought that was too minor of an issue to address … just like they thought half of the other points I felt may be important to the prevention of pokémon trafficking were unimportant, but that is neither here nor there.)
That having been said, species is definitely a major factor. Rarer species call for higher prices by default, with starter pokémon generally being so expensive they’re extremely difficult to obtain without a Symposium ID (which allows you to get one designated regional starter each per season for free, so long as you intend on giving them to trainers). This is largely because the amount of security needed to protect their breeding stock from pokémon thieves will play a huge part in how much that breeder charges. Of course, don’t get me wrong concerning rarity. More common species—which are typically bred for show purposes or for particular characteristics that are not present in their wild counterparts (such as specific fur colors)—can still fetch about 50000 pokéyen on average, and even then, it depends on which variations you’re looking for. It’s simply that rarer pokémon such as the starters and pokémon such as beldum and dratini are generally more sought-after on the market, which means they’re seen as being more valuable among breeders than more common pokémon.
Besides overall rarity, some regions have regulations concerning what you can and cannot breed (and in some cases, how many eggs of certain species you can hatch), so in some areas, certain species can be more expensive than they would be if they were bred and sold elsewhere—if they can be bred at all. For example, the entire continent of Australia has very strict regulations regarding which grass-types may be bred. Members of the shroomish line especially, given their tendency to spread their spores to mark their territory, are prohibited from being bred except privately and indoors. Meanwhile, starly can be bred in any region, but because they’re considered to be an invasive species in certain parts of the United States, breeders may only have a handful of starly readily available for adoption (as the regulations tend to limit how many starly they may have to encourage trainers to catch wild ones for the sake of population control).
Of course, as mentioned earlier, certain variations can affect price too. As a general rule, “shiny” pokémon (or those with alternate coloration) may fetch far higher prices than their normal variations, and genetic mutations such as pichu with spike-ear syndrome could fetch even more. Additionally, a pokémon’s special ability varies from individual to individual, and some special abilities are extremely rare within species. In some of these cases, the “hidden” special ability is highly valued, and a pokémon that possesses one may even be more costly than a shiny. For example, people generally value a torchic with Speed Boost more than they do a torchic with alternate coloration, and thus, the former will typically be more expensive than the latter.
And finally, you have custom orders. Very occasionally, a trainer may contact a breeder looking for very specific requirements. These tend to be the most expensive services a breeder can provide, as getting all of a trainer’s requirements may involve hatching many, many eggs, not all of which are guaranteed to find homes. Thus, if you wish to obtain a shiny Speed Boost torchic of a certain disposition, then expect to pay much, much more than you would an ordinary caterpie (a common pokémon that has absolutely no regional regulations anywhere in the world placed upon it).
The Pokédex According to Bill 