We've already mentioned motherboards, but that's not the only thing that mainstream manufacturers will scrimp on. Here are some (not all) ways they will try and make more money out of you:
Power Supply Unit (PSU) - your PSU, as the name suggests, is what provides power to the various components within your PC. They are a crucial part of your build. Firstly you have to make sure your PSU is able to provide enough wattage. Pre-built systems often include a PSU that is the absolute minimum required. This keeps their costs down, but would prevent any future upgrades to, say, a more powerful graphics card.
They also tend to be inefficient. At minimum your PSU should be 80+ Bronze rated (more on that here). This also makes them more expensive and, therefore, less likely to be seen in a pre-built system.
Storage - Both hard disk drives (HDD) and solid state drives (SDD) are areas that companies like to penny pinch. For HDD's, the area to watch out for is the speed (measured in RPM, or how many rotation per minute the disk is capable of spinning). 7200rpm should be the minimum, but you will often see slower drives, which would significantly slow down your computer, especially if the HDD is also used as your boot drive. For SSD's, pre-built tend to include really low capacity drives (if they include one at all). A SSD can run up to 100x faster than a HDD, but they are more expensive per GB. A low capacity SSD is ok for a boot drive, but won't allow for storage of many AAA games, meaning load times will be noticeable longer.
RAM - Firstly, any new system should be running at least DDR4 RAM. DDR5 is now also available, but it is still fairly new, comes at a premium, and there are a few bugs to be ironed out. I'm still surprised by how many systems still come with DDR3. What's the difference, I hear you ask? There are a few, but most important is speed of data transfer (rated in mhz) . This increases the performance of your system, by allowing the data to be stored within the RAM, and eventually re-read, faster. As a benchmark, you should be aiming for at least 3000mhz for Intel systems and 3200mhz for AMD's Ryzen CPU's. The latest Ryzen processor will use DDR5 memory only, and recommend speeds of at least 6000mhz.
You also need to factor in the RAM capacity. 8GB is common, but most AAA games today need 16GB to run smoothly.
CPU Cooling - planning on doing some overclocking of your CPU? Forget about it with most pre-built system coolers. They are cheap and they just aren't going to draw enough heat away from your processor. Building a custom PC allows you much greater flexibility. From air coolers with better heat sinks, AIO water cooled systems, as well as custom water loops, the world is your oyster.
