In my mind, Wonderland now occurs after Season 4. Yeah, I know the storm Will is walking through was supposed to be when the Wraith attacked Storybrooke, but that could very easily be retconned now. The final version of “Down the Rabbit Hole” makes no usage of Season 2 footage, nor even mentions the Wraith. In fact, it could easily be the storm the Darkness caused at the end of Season 4 instead. The only inconsistencies I can think of is that Will ends up dating Belle, while in Wonderland Will swore off love after taking out his own heart. He was also effected by the Spell of Shattered Sight, but you could easily argue that Will was just taking advantage of the chaos to pickpocket and get back at Hook. Still, this is one retcon I would gladly welcome, if it means Will retains his happy ending with Anastasia.