The first application I was told for this was that you were jumping over a sword, or a staff, and the juji uke was to then disarm the weapon. At the time, as a 16-year old in the mid 1980s, I accepted this explanation, but it's fairly blatantly ridiculous now (though there's no harm, every now and then, in doing a kata and pretending you're in a Kung Fu film, jumping over swords etc. - have some fun!). These days it's generally accepted that a turning jump indicates a throw (there are other hidden throws in kata with no jump, of course - the first appearing in Heian Shodan).
So why keep the jump? Surely it's silly to keep it in, and has only been put there to look good in competitions. While I think it's important to know the real meaning of the turn and jump in a Shotokan kata, I also think jumping serves a purpose beyond providing an opportunity for the more talented karateka to show off - it develops coordination, balance and athleticism, all good stuff in addition to the practical fighting aspect. It's also a great physical challenge, one - no matter what your personal physical ability - you can always strive to keep working at and improve.