Xbow should be the most damaging followed by Scythe/Bow.
actually I don't see that. forget about skill requirements and what not for a moment, think about how these weapons work. a scythe is a sharp blade at the end of a long handle, it was designed to harvest grains. it can cause some damage if you slice a person who is just standing there, but as with all slashing/bladed weapons won't get through most types of armor. a xbow fires a bolt, it can do some serious damage, can get through most types of armor(depending on range and type of head), but won't do as much damage or have as much range as a bow. force = mass*velocity, since an arrow has more mass than a bolt and is fired upward(to overcome gravity and get the range) it not only has the forward momentum but also the pull of gravity on it so it has higher velocity...meaning more force which means more damage.
the most damaging weapon(choosing from types of weapons in game) should be a spear. it takes all of a persons strength and focuses it on that tiny tip of the spear. the smaller the area you're hitting the more force effects it(hit a board with a hammer it might make a dent, focus that same force on a nail it goes through it), meaning it goes through all types of armor and the person inside...even better than your basic spear is your halberd, using the spear's shaft(don't say it) as leverage you can focus even more energy on a single point by attacking with the spike on the back of a halberd.
I will agree with you on throwing being op, but for other reasons. the weapon types and what not used for the skill make no sense. sure it was way cool when Xena threw a chakram(yes thats how its spelled) and it bounced around and came back to her, but warriors who used chakrams carried many of them into battle, wearing them like bracelets/necklaces until they were ready to be thrown. no thrown weapon(unless tethered which would cause slower attacks since you have to pull it back, and could even get you pulled into melee combat if you missed) was able to be used multiple times without collecting them after throwing. with the exception of certain types of throwing spears(such as a pilum) most thrown wearpons wouldn't even break through armor. if you're wearing armor made of metal, and some guy throws a rock(basic early throwing weapon) at you it might scuff your armor, but you probably wouldn't feel it unless it was a huge rock...
my opinion: the whole weapon system needs to be rethought! I doubt that happens though unless someone is making a new server from scratch, and I don't see that happening.