You will have to forgive me on this, but this is nothing more than growing pains felt by the airline and the passengers.
Meshing two IT systems together is like trying to mix oil and water. I worked in the airline industry when US and HP joined forces and sadly, to this day, there is still an east/west battle happening and that was at least 7 years ago. And I remember it took US's IT team almost a year to fix a lot of the problems it was having, both on our internal computers as well as the website.
Switching mergers, look at the DL/NW merger. It has been 3 years and their IT group is still having issues.
The problem with mixing fleets into unknown corridors makes it difficult to maintain a mx balance. Happened during the summer of 2009 with the new Delta. I could count on one hand how many of my roughly 65 flights actually went on time. Sure some had crew issues, but the majority of the delays were attributed to mechanical problems. Once the summer was finished, I started seeing less and less issues with mechanicals. I asked why, and was told that they needed every available aircraft during the busy summer months and once the summer died down, they were able to reduce schedules and formulate a plan that fell in balance with the new aircraft rotations.
I truly feel your pain, since I've already been through a merger on both sides of the counter. But I couldn't resist a status match. So here I am trying to do it all again.
And if you want some good reading head up to the delta forum and search merger and look at posts around 2009-2011. It's a great read and echoes a lot of your complaints and gripes.