Overall there are several reasons for that.
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First of all skin quality has improved vastly,newer skins usually include new particles and stuff like that,which means that they take more work to do.
However this also means that particle heavy champs usually get less skins than champs without many particles.
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On a similar note,there are some champs whose model is simply more complex.
This applies to Zac and his liquid body and jinx with her 2 swapping guns.(this is most likely the reason why it took skarner so long to get another skin)
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Some skins simply take longer than others.
They had for example some problems with Lunar goddess diana,the initial version was never shown to us,but was largely scrapped which is why diana took so long until she got her skin out
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The internal model of some champs is simply bad.
This is the reason why evelynn didn't get a skin for such a long time,because her internal rig is simply a mess(they managed to make safecracker eve because it was rather simple),same goes for rumble.
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Some champs are planned to get a major overhaul for their design/kit(or one on a scale that even riot isn't even sure of).
This is basically the reason why yorick gets ignored by riot.His kit is up for a major rework(that is currently not a priority,but they know they'll do it eventually) and his design might also get some bigger changes,so why waste time to make a skin for him if they might need to scrap a lot of that skin the moment he gets updated?
Popularity isn't actually that much of an issue,I mean just look at skarner,he is currently among the most unpopular champs,but he still got a new legendary skin.Skins take a lot of time and popularity comes and goes,so there is no guarantee for them that a given champ will still be popular once the skin comes out(in fact it is not uncommon for some champs to receive nerfs in the same patch they are getting skins).
Also you have to keep in mind that skins can also work the other way around,making rather unpopular champs more popular.
Not to mention that jinx is extremely popular,both as a character and as an adc and yet she still didn't get a skin.