Possible solutions:

Make Mudra uninterruptable, so they can be weaved between weaponskills.
(simplest option, but doesn't really simplify the job at all, and kinda goes against the point of ninjutsu)

Make Mudra collate on the client side instead of server side, so ping won't be an issue and you can hit them as fast as you like, then the resulting Ninjutsu is triggered on the server side.
(Probably the most tricky option, and this would likely require a load of testing and debugging, but it would probably be the most satisfying option for Ninja players, no massive change to gameplay, just a huge QoL update to Ninjutsu)

Rework the Mudra combo's, and remove Hyoton, so that all Ninjutsu can be executed with only 1 or 2 Mudra.
(Would simplify the job like they said and marginally reducing clipping issues, but wouldn't be a huge improvement)

Make Ninjutsu a GCD, so that you're only weaving the Mudra and not the Ninjutsu as well. Increasing all Ninjutsu potencies accordingly.
(Would change the flow of the job more than anything, and would be a simplification in some respects, but again, not a massive improvement, as you're only reducing your weaves by 1)

Rework Mudra to 2 and make Ninjutsu a GCD, the last two options together.
(This would have the greatest effect on flow, clipping and simplifying the job. It would achieve what they want better than anything, but it would also be the biggest 'hit' to the job for existing Ninja players)

Unrelated in some respects:
Have the bunny trigger automatically, instead of requiring you to hit Ninjutsu to 'use' it.
Have the bunny reset Mudra cooldowns so you can try again immediately.