Transcendence is definitely within the top ranks of issues needed to be solved. Granted it isn’t the root of the inbalances felt in the game, but it certainly amplifies them, making the divide wider.
If we take transcendence out of the picture, we can actually see that weapon atk power balances out with the attack power gained from core stats. R8 base 400-500 p/matk weapons is equivalent to the p/matk power a character will gain if they choose to invest their core stat. It is balanced in that regard.
However, with skill damage reaching thousands, it already severely hurts both core stats and itemisation. Now they add transcendence to the mix, increasing the gap between weapon/equipment vs core stats, worsening and leading to the issue we have now, INT/STR being underpowered and worthless.
Next is the issue of balance between classes, transcendence may have helped classes become viable, but the same equipment used by the already balanced classes increases the divide even more since they deal more damage in the beginning.
Transcendence is a good idea for end game imo, but it is pushed out far too early at this stage of the game. It should be kept at least till R10 is out, and all the classes are already balanced. Having it out now is just increasing the problems the game already has. Which is why my recommendation is to change how the current transcendence work, provide compensation to those who are invested in it. When R10 is out then reintroduce the same equipment enhancing system, at that time where (hopefully) everything is balanced then this system will be a boon rather than a bane.