At the end of the day, it really depends what you want to use the computer for and what your budget is.Custom built computers originally were cheaper, now its always more expensive and has warranty issues. They are fun to put together when they work, however very often especially with high-end motherboards their are many firmware issues and compatibility issues. You have to do proper research and make sure you have all the right components. Once that's done, the actual building and assembly of the PC is fun.Be prepared to have a budget in mind and figure out what takes precedent and whats a higher priority for example if you want to spend $1000 you have to decide if you want a more expensive motherboard, better ram, better psu etc. You can spend $50 on a graphics card or $500.
So in summery, it seems the best thing to do is buy something decent and upgrade it myself.