On most newer cars I've thought most OEM systems are probably the best all-around. Generally anything that increases power also increases efficiency so something relatively simple like an intake or exhaust they're going to spend tons of money finding the best balance. It's no longer arbitrarily routing some thin hdpe to get it from the intake box to the TB. I'm sure they take all of the fluid dynamics into consideration from the intake to the exhaust exit to try to maintain (or as close as possible) a smooth, laminar flow from idle to WOT. Though there is almost always some audio tuning as well to help the intake meet the characteristic of the vehicle. A Challenger can and should make more noise than a Caravan.
Intake side, yes, exhaust side ... ehhh ... they get cheap on stuff with the exhaust and sometimes it doesn't always mean efficiency.
My STI has a 2.5" mandrel bent exhaust on it from the factory. An exhaust does virtually nothing but make noise on these cars. The downpipe on the other hand is absolutely a "WTF" moment on Subaru's part. I believe strongly they purposely choked the wastegate exit flow to force the boost threashold higher in the RPM band so the engines would do better on MPG and emissions. A bell-mouth 3" downpipe is worth about 500 - 800 RPM worth of earlier spool, better boost control, and considerable gains in power (5%).