They've said in the past that it is for champions that have had the one of the larger impact that year (season). I think that answer leaves a lot up for interpretation and there are obviously a lot of other factors that come into play: Thresh only had one skin before last year's championship skin, same with Elise. Shyvana hadn't had a skin released in awhile, same with Morgana and both had seen extensive play during both splits, though Shyvana was mostly Spring split. Assuming the process would take 2-3 months, you have to assume the cutoff is going to be around the July/August for champion influence on the split. I believe that was also around the time that information/rumors about Shyvana getting a new skin, and it being the potential championship skin, was announced - so that seems to hold some weight.
I have no proof of this conversation, but I was brainstorming who the skins were going to go to before they were announced with a friend on Steam. I eliminated all champions that had a skin released in the last six months, and picked two champions from each role that had seen extensive play (that also didn't get crossed off from the aforementioned list). Morgana and Shyvana were both on that list, though I thought for sure we'd potentially see an ADC (Tristana or Kog'Maw) or a mid laner, but Riot had other plans apparently. It would be amazing if they released behind-the-scenes information on how they pick skin concepts, how long the process takes, and just some more information in general -- I've been trying to push for some of these questions to get answered.