The merge file is used for our AppLink functionality. We have to merge the AppLink package's environment on every launch or we couldn’t pick up changes made to the AppLink package.
Some child packages (AppLink packages) forces a large Merge file to be created. This can slow down the launch time, as you are experiencing. There is no workaround other than stop AppLink the child package and incorporate the bits into your main package.
Most of the times we don’t see large Merge files but IE is one bad candidate for being a child package. An indication can be to look at the virtual registry files in your project folder. I have not investigated it very deep but I suspect a large virtual registry causes a large Merge file.
Now when I think about it, sometimes there is a lot of rubbish captured in the registry. Try cleaning up the registry to see if that helps. The tool ThinAppHelper can be of assistance here. It lists the virtual registry in a nice tree view.