Hi,
There could be several reasons. I haven’t done any side by side tests for a definitive answer, but it could be that just using the newer plugins have increased the size of the app.
Also, in ME uses the www folder to upload, regardless of what is being used or not, so it is a bit easier to get resources in the app that do not need to be there.
One thing to note, in the res folder where are all the images are held there is a hidden file called .pgbomit. PhoneGap build uses this file to omit anything in that directory in the build. It is used in that folder so graphic resources for Android don’t get included in iOS builds, iOS into Androids, etc. If this file is deleted all graphics will be copied into each platform.
Here is a quick screencast to show you how to show hidden files: http://www.screencast.com/t/9Y9EqWpmklz4