Played around with this question for a while. It's tough to answer for a few reasons. Most importantly, it looks like -- for the majority of acquisitions -- the smaller studio is simply absorbed into the larger one. In other words, the studio 'disappears' after it is acquired. Only in a handful of cases did studios remain independent. For example, after a 1995 acquisition, "The Weinsteins operated Miramax with more creative and financial independence than any other division of Disney, until 2005 when they decided to leave the company and founded The Weinstein Company." (http://en.wikipedia.org/wiki/Miramax_Films)
Beyond that, I only have data on about ~2,000 movies that had sufficient critical/user reviews to include in the analysis.
With those qualifiers aside, here are a few data points. The scores are listed as critic/user:
* Columbia Pictures, acquired by Sony in 1989. Before 84/79, after 54/62.
* Miramax Films, acquired by Disney in 1993. Before 89/87, after 76/74.
* New Line Cinema, acquired by Turner in 1993 then merged with Time Warner in 1996. Before 68/82, after 47/65.
* Paramount Pictures, acquired by Viacom in 1993. Before 80/78, after 64/62.
Just to call out a bias in the data, ratings for all movies decline over time (probably because every recent movie -- good or bad -- appears on RT). The average rating for movies released 1996 or earlier is 72/70, and after 57/64. Nevertheless, all of the above-mentioned studios (with the exception of Miramax) showed a meaningfully greater decline.
Very interesting question. Do you have a list of TW/WB's acquisitions? Based on Wikipedia, Castle Rock and New Line look like the most interesting studios to analyze.