As a completely uneducated and casual-player look at the job, my guess would be that they've tried hard to introduce a chain of abilities that "need" each other (e.g. trying to justify themselves within the context of the story they've built / mechanics they have or intend to implement in the future). I can understand the penalty aspect; they're giving us something to make our current tools more potent along with the addition of some new tools, so they've tried to balance that out against how much we can use it - fine.
Overall, though, the penalty just doesn't seem to fit the play-style. I suspect the cast-timers came into play because, you know, they'd already set that as an expected form of control, so people already know how it "works", but for me (as it seems for others too) that's ultimately 'broken' what I understand as the style of play. The complexity and depth to the BRD in 2.x came from the weaving of GCD and oGCD abilities based on what DoTs, effects and party status is at any given point in time. It's that understanding of managing those aspects that adds depth to the role and the fluidity of the play-style means that as a solo you can chain things along nicely and finish an encounter while still in control, while in parties you have to adapt to the makeup and abilities of the rest of the party, while still timing and weaving ("playing", for want of a less musical word) everything together and trying not to run out of TP.
What I wonder, is whether there's different 'penalties' that they could apply to the job while under WM that still makes it useful but keeps the dmg and utility decisions under control. The thing that comes to mind here would be to keep the cast time on WM (it's a song, we have the expectation that to sing you have to stop and focus - fine), but while under the effect your GCD abilities are buffed (maybe more than 20%), but your GCD timer is longer - say by an extra .5 - 1 second. This way we hit much harder with our GCD abilities, and we can still weave our un-buffed oGCD abilities into the mix, but we can't spam our heavy-hitters for uncontrolled dmg (our characters fire an expensive round, and then have a longer 'refocus' period before they're ready to do it again). The bonus we'd then get for being in the stance, would be to have the new utilities, such as IJ, available to extend the effect over time of our buffed abilities (although perhaps using something like IJ should then force us out of WM stance, or decrease the WM buff over usage to keep it from being a "god-mode" so that we then have to manage the choice of doing buffed heavy-hits, or extending DoTs depending on the scenario).
The overall dmg output aspect, while annoying, is much simpler for the devs to fix and tweak, but the play-style is what's going to hurt this more than anything over time. So, SE, my feedback to you would be; please, please, please re-invest in understanding how the job plays and don't be afraid to slip-in some new play-style mechanics in order to manage the mitigation of overpowering a job though new abilities. While you've got established mechanics for controlling output (cast timers), they don't fit with the job role and play-style you're trying to attach them to, so you could do with finding something that does fit and applying it appropriately.
</uneducatedRant>