The most important thing to do in order to future proof a series is to get the series made in the first place. That means keeping the budget under control
I think you are approaching this thread with a specific agenda.
I am talking about once a show is greenlit and say a TV network has agreed to a 13 or 26 episode order.
TPTB saved all of the TV series original camera negatives and now it is paying off for TNG-R.
This thread is a hypothetical type of thread that deals with when
a scenario is already in play.
100 episodes in HD is a lot more future proof than 13 episodes in 3D at 4K.
Since season 4 of ENT shot in HD they won't be going back to shooting film since almost all TV episodics are shot in HD now.
Since we all know that there is a built-in Trek fanbase that will buy Trek product if it is a 2-season show or a 7-season show we are takling about futureproofing it beyond
one generation of home video release and the first HD broadcast.