Paid Time Off. 5 holidays off throughout the year..."because it's a retail company." Partners start off with 2 weeks (10 days) of vacation, 40 hours of sick time, and 3 personal holidays. It's not terrible, but you don't get an increase until your eighth year, and the lack of given time off around holidays requires the use of the majority of PTO around those events (Christmas, Thanksgiving, Easter, Memorial Day) if you wish to spend a little time with family. Salaried partners are expected to work 50 hours a week. If you work less, then you're generally expected to use PTO.
Company culture. I often hear this trumpeted as a positive within the community. I'm sure it is a positive to the majority of the 80,000 employees, because the focus of the culture is to make the hourly wage earners feel valued (primarily store employees and drivers). While I don't disagree with their value, I feel that the salaried employees are not valued here.
Systems - each organization has been allowed to procure their own information systems for their respective area. This approach has created a nightmare scenario for IS and Accounting. Many of the systems do not communicate with one or another or back to the GL. The expandability and often maintenance of these systems requires outside consultants or OEM support, which means the many of the needed changes never happen.
Cubicles. Need I say more. I know it's the norm, but I hate them so much.