You've hit on *the* 3 things I think really need to be fixed in
pui-list-packages.
>>>> "CW" == Christoph Wedler
<wedler(a)fmi.uni-passau.de> writes: 
CW> 
>>>>> "GK" == Greg Klanderman
<greg(a)alphatech.com> writes: 
GK> try this.  i submitted to patches last
night but haven't even gotten
GK> the usual (immediate) confirmation.  i will resubmit.
CW> 
CW> Thanks, now it doesn't delete some packages anymore.
CW> 
CW> But it now adds packages I hadn't previously installed (including the
CW> Mule files which are added to xemacs-packages/ and not mule-packages/).
This is due to also grabbing the packages required by a package, which 
I personally hate.  Also, I dislike that it never asks where to
install packages.
CW> It also didn't update to reftex-3.41, for example, as the 21.0-pre14
CW> announcement of SL Baur (1.10) would suggest.  In fact, my
CW> package-get-base.el (Sep 29 23:19) says s.th about author-version 3.38.
CW> 
CW> Just curious: does selecting the menu item (updating packages)
CW> checks whether to update the package-get-base itself?
No, currently it does not.