This is correct: due to layouts, snippets and extra functionality the package is bigger. Consider removing unused and excluded items.
Are there a lot of .jar files in your userlib? I remember that the conversion from 4 to 5 added a lot of jars and not all them are necessary. Can you compare the packages in more detail by unzipping them?
I'm facing the same issue at the moment. Upgraded from 4 to 6.5.1. MDA filesizes went up from 14mb to 115mb!.
Opening the MDA files with 7zip for instance can show you where the big files are. In my case there was a folder called Bundles and had a project.jar file in there of 53mb. Apart from that, it had a folder named sampledata that's 143mb...
Any idea what the project.jar is and how the sampledata got in the mda? I've got a zip file with data that is the same as the sampledata in 2 dirs: A datasnapshot and in the subfolder "documenten".
Would removing any of them decrease the MDA deployment package?