I get what your saying but the logic behind your examples is wrong; Avengers was a new universe different to that of X-Men, Spiderman, Fantastic Four and Man of Steel is separate from the old films and while its potentially the basis for The Justice League its a different set of stories from the Nolan Batman.
The only one which is remaining consistent is the new Star Wars, the X-Men films diverged and now they are trying to force them back together but it doesnt fit (case point, when did Prof X loose the use of his legs?)
I think Paramount did the right thing wanting to start a fresh, I still enjoy the old Trek but some of it hasnt dated too well and it would be a headache to keep everything straight without becoming a problem.
"Come, come, Mr. Scott. Young minds, fresh ideas"
In other words, right call lets bring on Star Trek 2 and 3!