Though your recording can be enhanced with EQ and effects, your fundamental building block is the guitar itself. This is where a lot of problems start. For session work, I often borrow guitars that I know have the killer sound. Next, choose a good environment, such as a wooden room with nice natural reverb. Remember that carpeted rooms will usually provide a relatively flat or dead sound.
Ambience is very important to a good recording.
Walk around the room while playing the guitar and try to find a sweet spot. You might get a nice sound playing into a corner, for instance, where you have the benefit of sound reflecting off the walls. If you do use the guitar's internal pickup, use it sparingly and in conjunction with microphone. Typically, acoustic pickups are designed for and most effective for live applications. When it comes to recording, you'll want to use the best microphones you can afford, high quality cables, and a good mic preamp.