I have a PPA at:
https://launchpad.net/~paelzer/+archive/ubuntu/bug-872145-ssh-prefer-user-configured-key

I have tested and the "IdentityFile" directive in /etc/ssh/ssh_config
does not count as "user defined". I'd have preferred if that would count
as well, but for now at least preferring the "-i" is better than nothing
and it seems to not need a major overhaul.

But other than that, this seems to work.
Former:
$ ssh -i /tmp/testkey -v horsea "echo 1" |& grep "Will attempt"
debug1: Will attempt key: /home/paelzer/.ssh/id_rsa RSA ... agent
debug1: Will attempt key: ubuntu@cpaelzer-bastion RSA ... agent
debug1: Will attempt key: paelzer@lap RSA ... agent
debug1: Will attempt key: paelzer@swarm.n RSA ... agent
debug1: Will attempt key: /tmp/testkey RSA ... explicit

Becomes:
$ ssh -i /tmp/testkey -v horsea "echo 1" |& grep "Will attempt"
debug1: Will attempt key: /tmp/testkey RSA ... explicit
debug1: Will attempt key: /home/paelzer/.ssh/id_rsa RSA ... agent
debug1: Will attempt key: ubuntu@cpaelzer-bastion RSA ... agent
debug1: Will attempt key: paelzer@lap RSA ... agent
debug1: Will attempt key: paelzer@swarm.n RSA ... agent


@Rob - could you give the PPA a try and report for your case the following once 
for the old and once for the PPAs ssh binary?
 $ ssh -i <yournewkey> -v <targethost> "echo 1" |& grep "Will attempt"

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https://bugs.launchpad.net/bugs/1872145

Title:
  explicit key offered after all agent keys, auth can fail before
  explicit key used

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