Just my observation and any concerns stated are purely my own and may be totally in error
Factory guards require you drill at least on hole (the top one) in the fender lip and then use the existing liner screws for the bottom. The OEM also seem a little more rubbery and flexible and *may* be quieter when running on wet roads with the water splashing on them, they may also be better (less likely to stiffen and break) in areas where you get a lot of extreme cold and winter slush packed in between them and the tire.
I went with the WeatherTech as they are drill free using the existing liner screws on the bottom and the top has a nice clamp type of arrangement. I put all four on in about 15 minutes. They appear to be made of an ABS type of plastic which allows them to fit very well but when the tires are throwing water at them you hear it (its not bad though). And although the plastic they are made out of seems durable I don't know if they will be brittle and possibly break in extreme cold when slush gets packed around them however I live an area of Washington State where that would be a very rare issue.
I had husky ones first, then took them off for fender flares and recently took those off for weather tech which fit much better and are more stylish.
P.S if you remove gender flares dont try and rub off any remaining sticky residue while washing the truck, you will scratch it.
I can speak for the factory flaps since I just installed them on mine. Driving in the rain I don't hear anything more than I did without them so maybe they're better in that respect. They're not a single flat piece of plastic like the Weathertechs, rather they're a molded plastic with two distinct sides and about an inch of space between them. They come with a foam piece in that space, probably to quiet them. You do have to drill two holes for each one. The instructions say to use this stuff https://www.amazon.com/gp/product/B000QIXDEQ/ref=oh_aui_detailpage_o08_s00?ie=UTF8&psc=1 on the holes after you drill to prevent corrosion.