Why were the rules for Proliferate changed?
According to a post from Mark Rosewater (Lead Designer for Magic: The Gathering), the reasons were to make the mechanic as a whole more easily understandable, along with seemingly wanting to streamline the experience in digital MtG games.
Quoting the post in its entirety both for reference and relevance:

R&amp;D is always on the lookout for ways to make cleaner, more straight-forward mechanics. This makes mechanics easier to process in tabletop and lessens the amounts of clicks on digital.
When we decided to bring back proliferate, we realized we could make a simple change that would both, on average, make the mechanic more powerful and clean it up for digital.
Previously if a player or creature had more than one counter, you the owner of the proliferating source chose which one of the different counters to duplicate. This new version doesn’t make you chose, but instead duplicates all of them. Remember, you still choose which players and/or permanents to proliferate.
Yes, there’s a tiny scenario where you have to chose between duplicating both a positive and a negative counter, but that’s far less likely than the scenario where you have two different types of counters you want to duplicate (especially on creatures as +1/+1 counters and -1/-1 counters negate one another).