The Junior Cert is seen as a test for the Leaving Cert, get students used to it. It tests the first three years of knowledge, the Junior cycle as it's known. You don't need a certain number of passes but it can determine the level you do your senior cycle subjects at (and therefore Leaving Cert). If you dropped from Higher to Ordinary in a subject before the JC, you almost certainly won't be allowed study it at higher for the Leaving. Also for schools big enough to have several higher and ordinary classes in the same subject, you might need higher than a C to be in the 'top' class of higher etc. ie. the one that goes at the fastest pace and has the best teacher. You have to do as many subjects at Higher as possible to ge the most points, so it's somewhat important not to drop levels if you can avoid it and do well.
It also helps determine subject choices for leaving cert and helps show what you're best at. It's incredibly broad, to determine strengths. All students MUST study Irish, English, Maths, a third language, Science, History, Civics and Geography. In religious schools, it's an exam subject too. The you have your two 'options', none of which are 'soft'- Music, Art, Business Studies, Home Ec etc. So 10 subjects for all, 11 for a good proportion. It's tough but sets people up well for the difficulty of the Leaving Cert. It has no bearing on uni at all, because all of the compulsory subjects for uni are studied at leaving cert level.