Mylar is fine - until dirt gets underneath or the inserts start bubbling. That's when it starts to drive me crazy. Yes, it's there to protect the playfield, and yes - I think it slows down the balls. But sometimes you gotta give a little to get a little....
You'll be fine to play without the mylar protectors. Wax the area and you are good to go. As far as replacement, that's up to you - a lot of folks will recommend replacement of the high wear areas (like in front of slings), but others don't think it's necessary in a home use environment.
Just be careful and research the methods for removing the mylar. Don't just grab a curled corner and pull or you will regret it immensely......