Like badMojo69 I used Smart Switch, and haven't had any problems. Since there are people who transferred over apps, messages, images, videos, etc using Smart Switch, and haven't had any problems I don't see any evidence that can blame Smart Switch itself. I don't believe number of apps transferred over would have any significance either unless you start storing those apps on a very slow SD card and executing from there. I had no duplicate apps after transfer, and if I recall correctly I believe I even saw Smart Switch mention that if it detected the same app already on the phone as the one being moved over it would not move the one from the old phone. I also believe Smart Switch reported that it copies apps over, but not the app's settings.
torbatch1, Can you say for sure that you experienced the problems directly after Smart Switch and that you hadn't loaded up some problematic app in-between copying over the apps with Smart Switch and encountering your lag? Are there any apps you launched before your lag/slow experiences before that you didn't launch before testing this time around? Did you configure any of the apps (or settings for some of the Samsung/Google apps) in a certain way the first time, but not set them the same way after your reset. There are a lot of variables unaccounted for. I suspect it is not the copying of the apps that caused your problem, but some setting you set in one (or more) of those apps (or the Note 7 settings) the first time around that you didn't set the second time after your system reset.