One of the main things that made me prefer Wicker Man to Megafobia was that I felt it flowed better as a ride than Megafobia due to the transitions not being quite so jolty. I felt that whenever Megafobia turned, it felt almost like a wild mouse coaster in style due to the jerkiness of most of the turns. Not all of the turns were like this, but most of them were. Whereas with Wicker Man, I felt that the ride's transitions rode really nicely and flowed really well (even the unbanked ones!), although the GCI trains might have helped in part with that. I heard somewhere that the Millennium Flyers manuoevre much more smoothly through the ride than the older wooden coaster trains because they are more flexible and are much more closely intertwined with the track, whereas the PTC/Gerstlauer trains sort of shunt their way through the ride, if you get what I mean.
I also found Wicker Man to be quite a bit smoother than Megafobia, but I suppose it's going to be as it's 22 years younger than Megafobia. Megafobia isn't really, really rough (I've ridden steel coasters rougher than Megafobia), but WM was a lot smoother, in my opinion. It's kind of like comparing the drive quality of a brand new car and a 10 year old car with high mileage, in essence.
Furthermore, I still found Wicker Man to be quite an intense coaster, even though it was smoother than Megafobia. Most of it was quite forceful, especially the first two interactions with the structure and the bits between. The not-so-Boring Corner wasn't even that boring! The ride still flew through it at a decent pace.
However, Megafobia was slightly more intense than Wicker Man. I also felt that the airtime was stronger on Megafobia. Megafobia was second only to Mako in terms of airtime in my eyes, whereas there wasn't that much on Wicker Man. There were two pretty good pops of air following the not-so-Boring Corner, and there might have been a subtle pop or two in the first drop, but other than that, there wasn't really much on WM. But GCI coasters strike me as the sort of coaster that can still be world-class without having tons of airtime, as WM definitely is.
P.S. Sorry for the long post.