It doesn't make a lot of sense, the original GAC was already quite capable of storing different versions of assemblies. And there's little reason to assume a program will ever accidentally reference the wrong assembly, all the .NET 4 assemblies got the [AssemblyVersion] bumped up to 4.0.0.0. The new in-process side-by-side feature should not change this.
My guess: there were already too many .NET projects out there that broke the "never reference anything in the GAC directly" rule. I've seen it done on this site several times.
Only one way to avoid breaking those projects: move the GAC. Back-compat is sacred at Microsoft.
I also wanted to know why 2 GAC and found the following explanation by Mark Miller in the comments section of .NET 4.0 has 2 Global Assembly Cache (GAC):
Mark Miller said... June 28, 2010 12:13 PM
Thanks for the post. "Interference issues" was intentionally vague. At the time of writing, the issues were still being investigated, but it was clear there were several broken scenarios.
For instance, some applications use Assemby.LoadWithPartialName to load the highest version of an assembly. If the highest version was compiled with v4, then a v2 (3.0 or 3.5) app could not load it, and the app would crash, even if there were a version that would have worked. Originally, we partitioned the GAC under it's original location, but that caused some problems with windows upgrade scenarios. Both of these involved code that had already shipped, so we moved our (version-partitioned GAC to another place.
This shouldn't have any impact to most applications, and doesn't add any maintenance burden. Both locations should only be accessed or modified using the native GAC APIs, which deal with the partitioning as expected. The places where this does surface are through APIs that expose the paths of the GAC such as GetCachePath, or examining the path of mscorlib loaded into managed code.
It's worth noting that we modified GAC locations when we released v2 as well when we introduced architecture as part of the assembly identity. Those added GAC_MSIL, GAC_32, and GAC_64, although all still under %windir%\assembly. Unfortunately, that wasn't an option for this release.
Hope it helps future readers.
Source: Stackoverflow.com