Thank you for your suggestion. However, the changes you are requesting
aren't really a bug and require more discussion, which should be done on
an appropriate mailing list or forum.
http://www.ubuntu.com/support/community/mailinglists might be a good
start for determining which mailing list to use.

There are a couple additional comments I would like add:
* The program isn't technically executing as the result of a +x flag or 
anything like that, nautilus is actually calling a helper application and 
running it that way.
* naitilus can be set to open the file rather then run it if you go into the 
configuration, I believe the out of the box behaviour that they want is to have 
the file run. 
* Java is generally pretty safe (although I am sure someone will post something 
to prove otherwise).  Even if a malicious file was run the hopes are that the 
user isn't running the file as root (he/she would have to enter a password 
regardless) so the whole system would be affected...

I am wishlisting this issue as it is a valid one and I can see the
reasoning from both sides.

** Changed in: nautilus (Ubuntu)
   Importance: Undecided => Wishlist
       Status: New => Triaged

-- 
Opening a Java Archive (.JAR) file executes it regardless of the "executable" 
permission bit
https://bugs.launchpad.net/bugs/313439
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