It's all about seniority. The more senior a pilot is at an airline, the better the quality of life...for the most part.
Seniority starts the day a pilot is hired and is tied to the airline...in theory. More on that in a second.
I currently have a whole 3 1/2 years seniority at my airline. As long as I stay at my airline my seniority will increase. If I go to a new airline I start all over again. I can think of no other profession where one can have 20 years of experience, change employers and start back at the bottom in terms of pay and quality of life.
When airlines merge integrating the pilot groups is as simple as cut and paste. If Pepsi Express bought Coke Airways, Pepsi would staple all of the Coke pilots to the bottom of their list. Coke pilots would be junior to all the Pepsi pilots even if Coke had been around 30 years and Pepsi just 3 years. Well that's how it used to be.
There have been countless examples of seniority list stapling and the horrible effects of it. Because of all the bad blood stapling is no longer allowed. Now when two airlines merge they are supposed to merge the list.
US Airways merged/bought America West in 2005. Three years later the two pilot groups finally voted on a single bargaining agent (union). There are still issues between the two groups formally known as East and West.
Continental and United are just getting started with SLI. It's going to be tricky as Continental has a much tighter scope clause than United.
Republic Airways is a mess. Republic Airways Holdings has the following airlines: Republic, Shuttle America, Chautauqua, Frontier and Midwest. The last two are new. Republic is still working on integrating Frontier with the rest of the pilots. All Midwest pilots were furloughed. Frontier has only been around since 1994. Republic has been around since 1973. Frontier is a "Major" airline while all Republic operations are "Regional". Should a Frontier Airbus First Officer hired in 2004 be senior or junior to a Republic E170 Captain hired in 2000?
Pinnacle, Mesaba and Colgan are all working on SLI as well.
The number of regional carriers is shrinking dramatically through consolidation. This should reduce the amount of whipsawing (pitting airlines against each other for cheaper feed/cost) as there are fewer players.
Seniority isn't just about pay. Seniority affects pay, vacation, scheduling, equipment, and retirement money (via pay). One seniority number can amount to thousands of dollars over the course of a career. I've heard several stories of pilots who were First Officers for months or years while a pilot ONE senior to him was Captain for all that time.