Easy answer ... way less expensive.
Now, once you decide you are going to DIY the exhaust, the next step (if you're someone like me) is to engineer the system. So materials (Stainless Steel), diameter / length, resonator or not, and muffler geometry all get studied.
It's actually not that hard. Inevitably you should get some performance improvement over the OEM system, but it's important not to build a "racing" exhaust for a daily driver. Proper scavenging, torque powerband, etc have to be taken into consideration.
My Miata and my RAM both have modified exhaust, from header to tip, all Stainless Steel, new High Volume cats (yes, I leave them in the system) followed by a resonator and then the muffler and to the exit of the vehicle. Details like the exit tip clearing the bodywork properly (a FMVSS requirement) and minimum lengths are taken car of.
I use software to help design the exhaust (the SW deals with the entire motor) so I know what the effects of diameter and length are (for example) and it's important to remember that any change in exhaust also means a change in intake (or vice versa) so rather than let that fall where it may, the breathing of the motor is also addressed.
But cost, aside from my time? Headers, cat, stainless piping, stainless resonator, stainless muffler and some welding, total cost per vehicle well under $C 500.00 [$US 380.00], Magnaflow and Hooker cats and mufflers, fabricated resonator, eBay (China) headers.
The Engine Design software is $US 500.00 a license, and that has to be taken into consideration as well, but of course it's used for a number of other alterations so it's not exclusively amortized on the exhaust system cost. Use whatever method you like to account for that. Based on what I've spent on the engine(s) as the % allocation of it's cost, it's about $25 (5%) but you could include the whole amount if you like; it's up to you. It's still cheaper than just one Cat-Back system and labour at a competition muffler shop (mandatory if you are buying performance exhaust; don't go to the local Midas).