You'll need a timer. There is no way to temporarily stop the execution of a script mid-way and then resume execution.
If you are using transitions as a slideshow as long as there is a 'fixed' length pause its fairly simple, you animate once with a start delay of the required pause. In the end effect event you change the target properties and trigger the transition again.
For a slightly more complex arrangement you have an array of info for each of the transitions (duration/delay etc) you cyle through this with a counter nice and simple. I have found that with the flex 4 transiotns that I have been able to remove timers almost completely from old code.
The following link is not done with states but its an exercise I did when seeing how hard it would be to move from a flash timeline to a flex swf using filters and amimations. The best part was that parallel transitions where much smoother than Flash(the frame rate remained consistant).
http://gumbo.flashhub.net/menu/ - source enabled
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Another possibility to explore: we enhanced the Pause effect in Flex 4 to optionally end when it receives a particular event. Not sure what you want to cue off of, or how you'd combine it with your other transition effects, but it's another tool in the box.