For my mind the best way to set up an irrigation system is with large-scale pop ups as they are easy to maintain and wet a large area with each one. In saying that the micro systems are great if installed correctly. The most important thing though is to be able to move each stake and tube when the plants grow so they don't disappear into the garden so don't use short pipe. Also remember that the system is part of the garden so needs to be checked and each stake moved and adjusted accordingly as the garden grows.
Another tip is to keep some reserve pressure in the system so if you need to add more heads you can. Drip systems or underground drip systems are fine if installed correctly and are placed in a standard garden bed that is not going to be touched. There are great spray drips if you need to do pots or hedge lines. Also remember that too much watering will wash away vital nutrients from the soil so be careful not to leave it on for too long. That is why making the system an automatic one can be important. I keep my automatic system set on a minimum setting and do manual bursts when the weather is dry.