Personally I have viewed Jump Drives as experimental technology, still being developed by the TSN. To me, the technology could have been gained through a number of different ways; espionage, trade, scientific discover, pulling apart alien vessels etc.
To my understanding, new weapons or ways of warfare have not been extensively used until they have been throughly tested in battle and refined. Consider for example, the development of gun powder weapons through to modern day firearms. They were used alongside traditional weapons for a while before eventually coming in to common usage on the battlefield. It it was much later that a move was made beyond lining up and firing at the on coming enemy to the modern day "fire and maneouvre" tactics we see today. Initially, they were unreliable, expensive or not efficient enough or in enough numbers to prove effective and therefore needed refining, testing and proving before being used more widely (the stages of development in firearms seems to be extensive; firing mechanisms, improvements in accuracy e.g. rifling, etc). Of course, the best technology seems to go to the most elite units first as well, usually due to the cost or expertise required to operate them.
Going back to the Jump Drive, there are several factors that I can see that can justify the Jump Drive as being experimental. You have to wait for the drive to charge before the jump initiates, they seems less energy efficient than warp drive, the loss of low warp is a detriment to maneouvring, it take time to develop tactics and confidence using the jump drive.
To me, the Jump Drive is still being tested and refined by crews of the TSN. When all the issues have been ironed out, then they may be issued more widely, or utilised on speciliast ships (missile cruisers?) or elite units.