The comparison of technology between an FMS and a flight planning system is like a basic calculator (FMS) and a top of the line PC (CFP).
The comments about the recency of winds in a CFP is misleading. A CFP uses a large data set of winds for various times and sophisticated atmospheric progression models to calculate winds and temperatures at the correct times as the flight progresses.
The wind/temp model in an FMS is very basic and the data is limited by what is entered and at no time will have the gird granularity of a CFP.
The FMS is a guidance tool to be used in concert with the CFP to fly the aircraft strategically.
Overall you are better to stick with the CFP, but we all recognize there may be constraints due to ATC and turbulence. Then it important to understand what is better for your aircraft, be a little high above optimum or a little low.