I find it ironic that Hawaii-based websites are focusing on the loss of wide-bodies as their major gripe regarding the acquisition - suggests to me ALK is doing a good job otherwise. The unfortunate reality is that there are simply not enough passengers willing to pay the premium, which is why HA required someone to save them from Chapter 11 / 7. This story has been around for a while now, I originally chose to ignore it.
As other have suggested above, seniority issues can be some of the most challenging to resolve in an acquisition; with the addition of more 787s in the near term, the issue should eventually take care of itself.
Bigger question should be the 717 replacement - ALK has been conspicuously quiet on this matter, will greatly impact both residents and visitors. More appropriate for such media to use their megaphones to prod management.