Fringe was able to make the shift it did because of a great writer's room. Fringe was a very special show, with execs that were huge fans, which kept it on the air.
I was also hoping for it to go into "holy crap we changed time too much" this season, too. Since imagine if they went back to the bunker and found it empty - or worse, found it occupied by government employees, what if the bunker had started to be used by NASA or whatever agency it belonged to?
But I am glad we will get the wrap up movie - and hopefully a time travel series with a fun cast like this that comes along later will do a nice mix of case of the week and overarching story (Person of Interest did the combination well for the first three seasons, then it went full bore into the overarching storyline for the last two seasons, which was *amazing*)