To clone an iteration plan, what i did is.
1.Initially accept project area to which it needs to be cloned through the wizard.
2. create the IterationPlanrecord and copy the selected iterationPlanRecord details to it.
3.using IIterationPlanService, I save the iterationplan to the teamarea which is by default first teamarea of the project area selected
am i missing anything.

The code to clone goes like this

IIterationHandle originalIterationHandle=planRecord.getIteration();
IRepositoryItemService repositoryItemService = getService(IRepositoryItemService.class);
IIteration originalIteration=null;
IIterationTypeHandle originalIterationTypeHandle=null;
IIterationType originalIterationType=null;
IIterationHandle workingCopyIterationHandle=null;
IIteration workingCopyIteration=null;
IIterationTypeHandle workingCopyIterationTypeHandle=null;
try
{
originalIteration=(IIteration)repositoryItemService.fetchItem(originalIterationHandle,IRepositoryItemService.COMPLETE);
originalIterationTypeHandle=originalIteration.getIterationType();
originalIterationType=(IIterationType)repositoryItemService.fetchItem(originalIterationTypeHandle,IRepositoryItemService.COMPLETE);

}
catch(TeamRepositoryException tre)
{
tre.printStackTrace();
}
IIterationType newworkingCopy=(IIterationType)originalIterationType.getWorkingCopy();
newworkingCopy.setProjectArea(targetProjectArea.getProjectArea());
IIteration newWorkingCopyIteration=(IIteration)originalIteration.getWorkingCopy();
newWorkingCopyIteration.setIterationType(newworkingCopy);
newWorkingCopyIteration.setDevelopmentLine(targetProjectArea.getDevelopmentLines());
newWorkingCopyIteration.setEndDate(originalIteration.getEndDate());
newWorkingCopyIteration.setStartDate(originalIteration.getStartDate());
//newWorkingCopyIteration.setChildren(originalIteration.getChildren());

workingCopyIIterationPlanRecord.setIteration(newWorkingCopyIteration);

and to save..
IIterationPlanService iterationPlanService = getService(IIterationPlanService.class);
IRepositoryItemService repositoryItemService = getService(IRepositoryItemService.class);
ITeamAreaHandle teamAreaHandle=(ITeamAreaHandle)targetProjectArea.getTeamAreas().get(0);
ITeamArea targetTeamArea=(ITeamArea)repositoryItemService.fetchItem(teamAreaHandle, IRepositoryItemService.COMPLETE);
workingCopyIIterationPlanRecord.setTeamArea(teamAreaHandle);
DTO_IterationPlanSaveResult saveResult=iterationPlanService.save(teamAreaHandle, workingCopyIIterationPlanRecord, null);
IIterationPlanRecord savedRecord=saveResult.getIterationPlanRecord();