The minimise animation is Metacity. You could try disabling compositing:
gconftool-2 --set --type bool /apps/metacity/general/compositing_manager false
and do logout/in. It should speed things up, but you'll loose certain effects.

Have you tried setting the env vars: QT_NO_FAST_MOVE, QT_NO_FAST_SCROLL to see 
if they help performance?
(sourced from http://qtunderground.org/wiki/Qt_Environment_Variables)

But other than those suggestions, your use case is very much a corner
case for us.

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https://bugs.launchpad.net/bugs/876491

Title:
  We should have a "reduced resources" settings for Unity 2D

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