I would say my custom parts are good enough for my application.
The PLA (which I use for prototyping) has enough strength, the ABS (which I will use later for final assembly) is even stronger (exactly the same material as LEGO). Although pins fit better in original LEGO beams, they fit well in my 3D printed bricks. This took some trial and error until I got it right. Everything is held together very securely. I did not print any studs, axle holes, gears, etc ... yet and for this project I don't think I will need to.
If I were missing an existing brick for some project I would rather buy an original LEGO brick trough 3rd party (like Bricklink) instead of 3D printing a replacement. Every time.