The BBC are restricted to only making a small percentage of programmes on iPlayer available on series catch-up. Also they need to have online rights to the series that allow them to do this.
The decision about which programmes should be stacked is probably partly based on popularity but I'm not really sure. The new series of Doctor Who will probably be stacked.
The search facility on iPlayer seems to work a lot of the time. Problems like you've found with Bad Education though are annoying.
If you search for "Gardeners' World" for example, the results will look like this
There are currently 6 episodes available so you get the most recent 3 and the "more episodes" button which will expand the list to show the others as well.
Also with series stacking there is a limit of 13 episodes of a series available at any one time. So when a 14th episode is broadcast, the first one is removed from iPlayer.