It's a combination of things that are making it feel wonky, but I think PB is what has really derailed MNK in 6.0; possibly always. The timing of it along with how Blitz works just makes everything all janky.
RoF reduced to 60s: Good
Brotherhood increased to 120s: Cool
PB split into two charges with a 40s CD each: Bad. Really bad.
Now what they have to do is go in and make all kinds of adjustments to get MNK back to feeling good again. Currently, I don't have any suggestions. I am still playing MNK every time I can log on because I want to be in the thick of this transition and these issues. I'm really glad I picked up MNK in ShB. A bit late, but at least I got to experience how it was before the EW changes.
PB's overall mechanic needs to be looked at. I am just not even sure if MNK needs what it does. I honestly think it can be nuked completely.
From my limited experience, MNKs flow seems to come from transitioning from form to form, and executing its positionals. Giving MNKs the ability to be free from these restrictions does not liberate its playstyle; it just makes it feel janky.
MNKs should be rewarded for proper positioning with bonus damage, and flowing through their forms to reward additional effects and beast chakra. If I am to make a suggestion, I would nuke Perfect Balance. I think this skill has been a bane to MNK for a very long time now, despite my limited time playing the job. I think MNK should always have access to all of their skills like any typical melee job, with one form unlocking the next. Then just make it so that executing the appropriate skill while in that form grants bonuses such as additional effects and a symbol for the Blitz gauge. I think positional requirements can make a return on skills that don't have an additional effect. Under this system, only Demolish and Twin Snakes would be free of positional requirements.
That said, I just think they are trying to do too much, and really need to focus on what makes MNK work instead of trying to redefine it every expansion.