Itoo make every attempt to get all the dust off the airframe before covering. After using compressed air to remove as much as possible, I also wipe the entire airframe down with a tack rag. Then again before covering each section/panel.
Ditto on the getting the film stretched as tightly as possible while attaching, minimizing any wrinkles or slack film. Then not a lot of shrinking is necessary.
I will admit covering with Monokote is not easy to do well, but if you practice and be patient it works just fine. Since I'm new to this hobby (this is my 3rd year of building &flying RC planes) I have no experience with the "old" Monokote but have had great success with the new stuff.
To be fair, my favorite iron-on covering is neither Monokote nor Ultracote. It's 21st Century Fabric. A LOTmore expensive but it applies well, and looks better on scale type aircraft, IMHO . AJ-3 Cub should NOT be shiny!
Mark