Just get rid of Classes all together and keep the skills.If the player wants certain skills he can obtain them from an npc,leveling up or leveling up said skill. Although there's be penalties for someone training magic who decides to wear heavy plate armor or a character who wishes to train archery/bow will take a penalty for wearing anything heavier then chain armor.

Just a thought,this coming from someone who has been playing Wurm Online since 2012. Just a passing thought.Probably won't cure all imbalance issues,but it'd might be a huge step in the right direction.