It's so simple.
1. You hire two of the nerdiest Trek fanbase who know the entire canon of Memory Alpha and Beta. They are your go to archivists for the writers so canon is preserved. Simples.
Memory Alpha is the official canon
http://memory-alpha.wikia.com/wiki/Portal:Main
Memory Beta is fan fiction which introduced some very useful information to fill in the blanks.
http://memory-beta.wikia.com/wiki/Main_Page
2. You set it 200 years in the future.
Most things can change and be explained as major events have resulted in major changes. Then shows which explain why they changed.
Up until now, Star Trek V was the most gobbledegook pure crap. Now STD makes that freakin' nonsense of Spock's half brother lookin' for God....looks like Citizen Kane by comparison. And William Shatner directed that wretched piece of garbag.
Edit
There is only one cure for a Trekker to rid this heretical scifi noncanon abortion from your awareness: watch great essential episodes.
Here is the binge list of the best episodes of Star Trek. It skips any that are bottle episodes on useless tangents.
http://www.denofgeek.com/us/tv/star-...-for-beginners
It breaks it down by series with notes, so you at a glance know which ones to watch, or ones you should have watched.