Ages is more puzzle oriented while Seasons is more action oriented. It's preferred you get both anyway since they link up together after beating one and inputting the end password into the other, making one large game.
If you're a fan of more classic titles like Link to the Past and the original game then Seasons is for you. If you're more into the 3D title games of OOT and MM then Ages would be for you, especially since Ages basically amounts as "OOT: 2D Edition." My personal preference is towards Ages since the Maku Tree is female (yes, that's a point over Seasons) and more importantly the time travelling nature of the game makes for some pretty interesting situations you need to resolve. (Like buying a seed in the present, planting that seed in the past to finally obtain the fruit the tree bears in the present.)