While I'd agree there's certainly a gap between the damage WSs can do, it seems to me the issue for the development team is really skillchain damage, something that heavily favors jobs like SAM (in frequency) and THF (in potency). One way to manage this would be to temporarily reduce the skillchain damage for a weaponskill as it is used repeatedly in a skillchain.
Example: A Samurai uses Tachi: Fudo alone to make Light skillchains repeatedly. While the first skillchain would do full damage, repeated skillchains using Fudo would grow weaker, gradually restoring to their full damage over time if the SAM alters his strategy. During this time, the SAM would probably want to use other weaponskills for their skillchain damage, or instead open a skillchain for another player using a different weapon altogether.
The potency/duration of this effect could be affected by the level of the skillchain, and how many weaponskills were used in conjunction. As such, a low level skillchain consisting of 2 weaponskills would not hinder the long-term skillchain damage as heavily as a 6-step skillchain that closes with a powerful Rudra's Storm and Darkness. This would not only increase the strategic value of other weaponskills, but encourages teamwork with other jobs as well, such as WAR or DRK who have a variety of weapon and skillchain options.

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