There has never been a better time to buy a power meter.  With some many new brands the price of a quality power meter has been driven down by intense competition.  Stages was one of the first to introduce a crank arm based power meter, a feat some brands touted as impossible place to get accurate readings doggedly sticking to the location they determined was "best" to place power measurement.  But the non-drive crank arm is very easy to replace/install, and keeping the price point well under $1000 brought power measurement to the masses.

Pioneer introduced their crank arm based power meter touting better accuracy and force measurement in more locations.  Their original offering only had Ant+ technology meaning it was not compatible with Bluetooth devices such as phones, tablets, and some PC's.  Your were mainly stuck with their clunky head unit and could not easily run apps such as Zwift or Trainer Road.  Stages was one of the first power meters to offer both Ant+ and Bluetooth signals.  

Both brands now offer single leg power meters within the same price range (which has progressively come down as I noted earlier).  Both offer power meters with dual signal output (Ant+/Bluetooth).  In terms of accuracy Stages states their Gen 3 as +/- 1.5% whereas Pioneer is 2%.  This is a negligible difference and in my experience consistency of data is more important than a small amount of accuracy.  Both address this with active temperature compensation which helps maintain data consistency.

Stages diversity of their products fairly crushes Pioneer with models compatible with most Shimano road and MTB cranksets as well as models for Cannondale, SRAM, FSA, and Campy.  Pioneer by contrasts makes units for Shimano Ultegra 8000 and Dura-Ace 9100 as well as a few others available for factory installation only.  This is one reason Stages has been able to capture a huge amount of market share by comparison; your bike may simply not be able to run a Pioneer power meter.

Stages has progressively slimmed down their power meter making clearance issues almost non-existent with their Gen 3 model whereas Pioneer is much bulkier in length and width which can create more clearance issues.  This is something you want to vet out on the front end before purchase if possible.

The main difference that Pioneer promotes is force detection from 12 locations using more strain gauges.  This allows you to monitor your pedal stroke force vectors in real time using their head unit or one produced by Wahoo.  While this data may have some use in the fitting process I greatly question its application to the end use.  Everyone has some level of asymmetry in their pedal stroke.  There is no perfect pedal stroke because people are asymmetrical.  They have a wide variety of biomechanical differences from left to right.  Most will have a functional or actual leg length discrepancies, they have a dominant leg, they may have a lower arch on one side, compensations from previous injuries to name just a few.  It is important to note that data is useless unless it has actual performance application.  Using this data to modify your pedal stroke on the fly may add up to more confusion than watts.  Some may find benefit in it, but I believe most will have little use for it.

We have been selling power meters for almost 20 years and one thing I don't recommend is becoming an early adopter of a new brand.  I have seen them come and go and in some cases the consumer is left holding the bag when it comes to warranty and service.  Because we have sold so many Stages power meters in comparison to Pioneer I can only speak to Stages warranty department which is excellent.  Most of the issues we had were with gen 1 and gen 2 units and they were still few and far between.  We have had only ONE warranty with a gen 3 which in my opinion is very exceptional.  

*Update 1/6/2020 Stages Cycling drastically dropped their prices, pricing most brands and models out of the market.  They are now selling single sided power meters fro $299.