Entropy: The best skill tree in my opinion. Early on Anomaly, Convert, and Diversion give you a strong deck-building advantage. It gets better in Tier 2 with the ability to now go Rainbow with Stellar Radiation as well as getting the needed cards with Anomaly II and Convert. You get an even greater edge in dueling with Diversion II and Confusion. Tier 3 just gets even crazier by not only forcing them to use certain Marks, but also blocking them from using key counter cards with Diversion II and then being able to pull from a sideboard in case he did something unexpected in your first game. And woe to anybody who doesn't have a Rainbow library to draw from if they face a Champion of Entropy. The only Champion that is better I think is the Gravity Champion.
Time: They have some meh skills but a few are real gems. The adventurer skill is nice since it allows you to finish the quest chain faster while picking up more things along the way. Foresight is a nice dueling advantage if used wisely. But to me, the best skill here is the Research skill. Use your first Relic to learn Digging to get more Relics (or just learn it permanently). After that, you have access to unlimited Relics to use for every Fast Travel which will help with quests; every crafting skill for access to every rare card; many deck-building and dueling advantages like Convert, Rising Storm, Summon a Creature; and many other in-WoE advantages like Shadow Jump, Mobility, Black Market, Trading. Clockmaker and Scholar (especially if this is any Tier 3 or down Skill) are great. The Champion skill is pretty good.
Tied for third is Darkness and Underworld. For UW, the stand out skills are Disarm, Black Market (if there are some really nice illegal items), and Trading. For Darkness, Summon a Creature is nice early on. Shadow Jump is fantastic. Mage Hunter is a killer skill and the Champion skill is devastating.
So basically, if you want to win by conquering, go with Entropy. If you want to win by questing, go with Time.