Accepting that there will most certainly be plot holes within the Red John story line that may never be resolved (if a show runs long enough, there will almost always be some continuity errors), I think it's more that fair to say that some of the gaps here go well beyond oversights or that can be dismissed (in the minds of the writers) as minor details.
There have been many postings outlining many, many questions to be answered - and some of these may simply the natural product of unresolved curiosity.
However, there are some clear holes in what have been central elements of the story line, plot elements which remain unresolved but that must have been considered by the writing staff at the time they were written, even if RJ wasn't determined until later within the show:
- The connection between Visualize & Red John, and how Bret Stiles in particular was so well versed in all things Red John, as well as the events at the Farm
- How Red John was able to generate such a loyalty among his minions, even, for some of them unto the their willingness to die for him
- How Red John did, indeed, come up with the List of 7 - or perhaps, more importantly, why he offered those names up to Jane & the CBI
- Why CBI Senior Management, each in turn, was so willing to report on Jane to Bob Kirkland / Homeland Security
There are hundreds of other questions, each of which hold our interest at different times, but these points have been major recurring elements within the plotline of the show.
Even the JJ LaRouche's 'Tupperwaregate' was brought to a meaningful and compelling close - do we really think that the core plotline will be left so open ended?
There must be more to come.