The first issue spotted in open beta is lack of player control. The post clarifies that this refers to "the inability to pick the types of mission and gameplay you like to play when you want to play them." The team intends to implement customizable, small-scale battles known as Fight Club/Proving Grounds matches. This should allow players to play what they want, when they want, making it perfect for people who are short on time or crew members.
Issue two is a big one: cheaters (and the perception thereof). The blog post takes a bit to talk about solutions to keeping cheaters from ruining the game for others. Moreover, there's also some discussion on some game features that are often perceived as cheating, but in fact are not, which should hopefully keep players from crying hacks every time they find themselves on the receiving end of a well-placed bullet.
The last issue is one of player motivation. The devs talk about the game's Threat Level, and note that while some people see it as a "progression metric and a community status symbol," it was never the team's intention for it to serve either purpose. The team discusses a few ways of changing this mechanic in order for it to serve its intended purpose, while also giving players a solid way to track their progression.
For the full and unabridged post with all the juicy under-the-hood details, head on over to the APB Reloaded dev blog and take a look.