It may be intentional design that certain iconic jobs are just easier to play and optimization is less important to the devs. If a new player can come in and do okay as a WHM or SMN or RPR, then the popular "entry level jobs" are performing as intended.
Put another way, and using casters as I think a pretty clear example, what if the devs' idea of "balance" is having a job for every level of skill?
* SMN - beginners, casual
* RDM - intermediate, prog
* BLM - expert, current raid tier and Ultimate
You can even see a similar spectrum across Maiming vs. Striking (although I'm not sure where NIN was *intended* to fall in that spectrum).
Does that obviate a hope that jobs can still be balanced at all levels of play? Not at all. Does that still suck for people who mained WHM prior to this rebalancing? Absolutely. But I do think it is important to keep in mind that there may be other factors at play. The more jobs we have, the less important job balance actually becomes if there are other prevailing priorities like accessibility.
I also have no idea how WHM plays at lower levels and if it actually *is* more accessible than the other healers. But I have a strong hunch it probably is the most intuitive of the healing jobs, despite all its inefficiencies, because compared to the other healers the concept is quite direct and gimmick-free.