The biggest issues with the system revolve around transparency and the rules that the company decides to implement.
To begin with, there is an ugly learning curve as it is not exactly intuitive to sit down and put in a bid. It really does pay to make time to learn the system and speak with any trainers or other help available lest you receive very unfortunate results. There are many different ways to the same results, so everyone will develop a different system. Take care in getting advice from fellow pilots, as differing seniority can produce drastically different results from the same bid. Again, it pays to talk to a trainer about specific bids.
The other issues are just the rules written into the software that the company chooses, presumably guided by the pilot contract. Things such as amount of trips left over after finishing the bid run can have large impacts. If the schedule is built to 0 open trips, the software has more difficulty creating legal schedules to accommodate everyone, which then means the software will rearrange schedules to create legal schedules for everyone. We refer to it as the splat. It is frustrating to see trips that you wanted go to those junior to you but are unable to get due to the computer not being able to develop a legal solution.
Finally, it can be quite difficult to prove that the software, or human interference, made a mistake. To do so you generally have to show that you could have flown the trip you wanted plus everyone junior to you would still have a legal schedule.
That being said, as a former continental pilot who has used the system for years, I have mainly figured out what works for me. Generally my bid doesn't take very long, because it is generally the same month to month with just different days off requested.
Summation: if you adopt it learn the system as best you can and get help, especially at first. Make sure you understand the limits the company is using to create schedules, if possible keep those rules contractual to prevent abuse. The rules make a huge difference.