I might be late to the party but I stumbled upon FSAerodata to update the default waypoints and such in P3D (and FSX). Supposedly this program makes the sim better since everything is up to date, it makes the airports more realistic because you can use correct SID/STAR procedures. But I do have one question to anyone who does have this program. Does it actually make the default ATC utilize ALL of the runways at an airport? Based on wind direction, time of day, flow of traffic type thing. Because currently I fly into several airports that have more than one adiquate runway, but my ATC only recognizes one runway no matter what the conditions are. So hopefully someone can confirm this program fixes that flaw...

The default P3d ATC is very rudimentary. It doesn't use SIDs and STARs. fsaerodata will update all the stock airports to the latest AIRAC such that it will match the database contained in payware aircraft navigation units. But unfortunately it doesn't do two two things. It won't make the default ATC any more realistic and it won't actually update airport runways if the physical layout has changed.

The next step up would be Pilot2ATC which will guide the user aircraft using the latest AIRAC, including SIDs and STARs. Unfortunately, any AI aircraft will still be controlled by the default ATC which can get a bit confusing. 

The next step up is VOXATC which does the same thing as P2ATC, but in addition both controls and communicates with AI aircraft. This level of realism is also fairly expensive as it requires a Navigraph subscription, an fsaerodata subscription and the purchase of VOXATC.

One last point, many stock airports have multiple runways, but they are not designed to support all of them. Airport Design Editor can be used to correct this oversight, but updating a lot of airports can get pretty tedious. That's one reason why people buy payware airports.