Did anyone ever come out and tell the secrets? Clearly, it’s not going to be picked back up again, so- why not?
You know- they should be required to put a “here is all the secrets” letter in a safe deposit box for these kinds of shows.
So despite that two “made for TV” Movies (which I saw,and the island onejust muddled things more) there still remain plot holes and mysteries?
That’s my understanding, yes. I recently re-watched most of the series (which I taped when it was rerun on TNT; I now curse myself for taping over several episodes), including the two made-for-TV movies. It’s one of my all-time-favorite television shows. 
We know that Miss Parker and Mr. Lyle are actually Mr. Raines’s children, and that homocidal insanity runs in Mr. Parker’s family (which would have explained Lyle, if he’d been Mr. Parker’s child), but we don’t know how Raines came to be fooling around with Catherine Parker. I can’t even remember right now if Mr. Parker is presumed dead, having jumped out of the plane with the scrolls and a parachute in the last movie. Jarod never found his Mom, though he caught a glimpse of her in the last movie.
In my opinion, the TV movies just created more questions.