Limited Edition skins were created as a "once in a lifetime thing" originally but Riot deiced to change that and re-release them since their player base grown massively and those skins were rarely seen. They gave those special features such as Borders and refunded the RP amount, originally, http://na.leagueoflegends.com/en/news/store/sales/plan-vintage-limited-edition-skins but wasn't received quite as well as they hoped. So when Championship Riven got her turn and they gave her a border, in-game crown and special ult effects. Which people seemed to enjoy a bit more.
Skins like Traditional Karma, Trundle and Sejuani however were always listed as LEGACY. Legacy being that they are available for a short time, and set to return again (usually yearly). https://support.riotgames.com/hc/en-us/articles/201752944-Guide-to-Legacy-and-Limited-Skins#h1q2 They are also always available through mystery gifting and hextect crafting, where as Limited Skins would not have been available in those until they were moved to the Legacy category. The Traditional skins though were made as a kind of thank you thing for players of the original look and feel of the champions, and thus they got them for free if they owned them before relaunch. However at that time they could also be purchased for 975 if you didn't already own the champion. So this is just a repeat of that instance, where they are once again available instore for those who don't own the skins but do have the champion. As in the end, they were Legacy, not Limited.
Things such as Urf The Manetee Warwick, Black Alistar, Silver Kayle, Young Ryze, ect are all still Limited Edition skins and cannot be gotten in any fashion unless you have a time machine to go back to the time they were first released. So there are many differences between Limited and Legacy.