In previous games, you had to do side missions to upgrade your respect level, as your respect level was the key to doing missions. This isn't the case anymore, but it's still a good idea to do side missions. The more you do, the higher your respect level goes. You'll need your respect level as high as possible to unlock upgrades via your phone. These upgrades can make or break your ability to do a certain main story mission. Take your time with these side missions before you really start in on the main missions.
Added by: Forgoten_Scars Nov 22nd 2011, ID#7996