Welcome to the board!
The Penn Flyer set has a couple more sections of track, and some trackside acessories to enhance the basic layout. Most online stores should be offering some special deals for the official start of the season. Nice to see that you are getting your daughter started early in our hobby with her own trains.

Larry

 It seems that both the Scout and Penn Flyer sets come in both conventional and remote versions, with the Penn Flyer having no less than 8 different sets and configurations to chose from!
Which sets (with product numbers) are you comparing?

You can run new and old trains on new and old track; everything is compatible.
To run your old trains on the newer FasTrack, you would need to disconnect the newer power pack from the track and connect your older transformer in its' place.
The newer LionChief trains can be run on the older or newer track with your older transformer set to maximum voltage.

Larry

Glad to help you.
I'm sure your daughter is familiar with remote controls at home, so she will be at home with a remote control train set.

The new power pack for the LionChief set has no variable voltage control like the older transformers do. They have a fixed 18 volt DC output which is all the LionChief sets need. The hand unit controls the speed with electronics in the locomotive.
The LionChief sets will also work with conventional AC transformers, but you set them to maximum voltage and again, control the speed with the remote, not the throttle handle like conventional locomotives.
The power packs for the LionChief sets have a DC voltage output, but have no throttle handle to regulate the voltage for speed control. In addition, any trains with whistle or horn sounds would sound continuously with a steady DC voltage on the track, as it is a DC voltage that triggers the sounds on conventional locomotives run on AC voltage. Therefore, the newer LionChief power packs would not be suitable at all to operate conventional trains.

Larry