If there are many errors on the package due to incomplete configuration of the controls, there would be many errors reported on the error list window. This error list keeps on getting updated at every change in the package. For example, there are 6-10 flat file destinations which are not configured with the input stream and placed on the package for future use. There would be dozens of errors reported on the package, which can be seen from the errors window. Then suppose if a sort transformation is placed on the package, BIDS will validate the entire package again and the entire error list would be refreshed again. This makes sense as BIDS is trying to find out if the change in package has impacted or rectified any errors present on the package.
So in essence, the time taken is more. And the time taken is for the entire process and not just placing of control on the package, though it might seem that just placing of control on the package is taking a lot of time.
The resolution is, disable all the control flow elements that have errors due to logical reasons or due to incomplete configuration. Unfortunately as there is no disable functionality in the data flow, remove all the tasks that have an error due to known reasons. Save the package, and try to execute it again. Now the package designer in BIDS should run much faster than what was the case earlier, provided you have quite a few erroneous tasks on the package.