I treat every Cat5/6 cable the same in the home. At the head end they go to a patch panel. At the room end they go to a wall plate. All terminated 568A.

Now i can make any RJ45 jack in the house be anything. It can be a phone, an ethernet jack or used with baluns for audio or video. In 5-10 years when we remove all the existing hardware we dont care what the Cat5s were used for. We can re-purpose them without removing a single wall plate.

The "pig tails" are a lot less work and it saves us from having to deal with the RJ11 keystones. They add time to each wall plate because you have to look on the list and see which one gets the RJ11. You have to remember to position it correctly on the wall plate so all the phone ports are on the left (for example). Its much easier to burn thru the rooms terminating everything RJ45 and worrying about what goes where later.

As an example lets say your Cat5 for the phone passed when testing but when you connect the phone to it you have noise on the line for whatever reason. If your wallplates have RJ11's you have to start spinning screws and break out termination tools. If everything is RJ45 you just move the phone to the other RJ45 jack and make a note about the unused cable thats having problems.