Was the removal of nonmagical BPS res and immunity a good descion?

So one of the biggest changes to monsters in 5.5e has been the removal of resistance or immunity to bludgeoning, piercing, and slashing damage from nonmagical attacks. 

The replacement was either buffing monsters who had it in other ways (like more HP or higher AC) or by making the resistance universal to magical weapons as well, and removing flat immunity to BPS. Was this change justified and a good desicion?

In practice, resistance to non-magical BPS was a non-issue in actual play.  By the time those sets of abilities proliferated drastically every single player was likely to have at least a +1 weapon (which is just an uncommon, non-attuned item, after all).  That meant there were wasted words on a statblock that did not really influence gameplay, which is a strong sign something should not be there.  Additionally, this was a minor annoyance and barrier to entry or new players, who might get bogged down on the distinction between non-magical, as well as a potential trip-up for experienced players who are so used to instinctively seeing these abilities as "nonmagical" they might instinctively read a non-existent "nonmagical" into a stat block when, in fact, it is supposed to be true resistance to those damage types.

Now, instead of a useless signal taking up space and informing the DM nothing of value, the signal is used when it actually matters, making sure this information is only provided when it is going to have a real influence on the game. 

If you really want monsters that can only be defeated in a special way, regeneration or other special death mechanics generally do a better job than immunity. I've used werewolves with regeneration 5 (prevented by silver), and it forced PCs to actually seek out a silver weapon, rather than relying on PCs who did non-physical damage.