It's mostly the whole revival scheme that always struck me as a bit outlandish given how adamant the story/lore has been about resurrection being impossible.

Even Elidibus was unable to be returned to the Convocation in the truest sense, with them instead receiving a primal approximation. If Zodiark couldn't fully restore a single Ancient, it would stand to reason that the others brought back would similarly not really be themselves and having a whole slew of primal-like entities could've been...less then desirable, assuming the actual act of restoration didn't pose problems in its own right given that it entailed Zodiark giving up the myriad Ancient souls comprising his being to replace them with other lives.