I am one of the supporters of the FreeNX project for Ubuntu and although
I cannot speak for x2go, I do know both the benefits and disadvantages
of FreeNX.  I am a proponent for FreeNX, but there are several problems.

There are indeed inherent security flaws that exist partly due to the
code base originally being forked from version 6.9 of the X server.
Although many bug fix patches have been applied, there is still no
guarantee that they are all applied, and because the base from which it
was forked is no longer compatible with the now more modular design of
X.Org it is harder to apply the patches that they have made to X to
incorporate the NX conpression technology into the current X server.
Also, if someone uses the default NX public key for communication (this
is not recommended, but many do), you open your server to the
possibility of hackers trying to hack current security flaws inherent in
the nxserver script which are unknown to us.  With the nxserver script
being the shell of the NX user, anyone using the key gains access to
this user and if an exploit is successful root access may be granted.
With FreeNX being an open source project, it could become an easy
target.  This is avoidable, but it still needs to be addressed.

However, the benefits of the NX compression technology and communication
protocols are very good and achieve near local responsiveness when
connected to a desktop through it.  The only other technology I have
seen that is equivalent or better is Citrix for Windows servers.

Although I agree with you Jo-Erlend that FreeNX is a very good thing for
the Ubuntu desktop in that it offers us a much better alternative to VNC
or RDP which are both inherently more flawed and even less secure. Due
to the age of the source files from which it was developed it is not
ultimately a good thing for us to continue longer than we have to.

A better solution is for us to extract the fundamentals of the NX core
technology and incorporate this technology as a modular and installable
component of the existing X server.  Fairly similar to how you would
install your video drivers or custom mouse drivers.  This is
considerably more work than what can be achieved in a single release, so
I do agree that in the mean time including the packages is a good
intermediate step towards ultimately a better X remote communication
technology, but should only exist as a stepping stone to our final
destination.

-- 
[needs-packaging] FreeNX
https://bugs.launchpad.net/bugs/183801
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