I've had both integrated and separate and both have their positives and negatives. Integrated amps can be very high quality and sound very good depending on what you get. Advantages are saving space and not having to buy an interconnect to connect the separates. If you normally upgrade your power cords, then you will also have that savings. Also integrated amps are built with synergy in mind so no worries about matching a preamp to an amplifier.
Separate amps and preamps have their own dedicated power supplies and chassis and have less likelihood of interfering with each other. Also, like others have said you have the added flexibility of only replacing one of them for an upgrade. Separates often sound better but this is highly depended on the comparison made and equipment.