The "but it makes the iPhone water resistant" is weak argument that even if true, could've had a simple manufacturing solution (ie. no need to have the bore go straight into body of phone where electronics are, have the bore cylinder sealed with only wiring running to logic board).
Tim Cook, much like Steve Balmer, is a brilliant operations guy that can make minute adjustments to product lineup to produce all sorts of incremental once-off sales. However, they both lacked a fundamental "product vision" that resulted in tactical gains and strategic losses. Apple once again needs a product visionary.