I completed my EPQ in Year 12 (but ran over a little into Year 13) and achieved an A* - for me, it was just as valuable as some of my A Levels in applying for university. The skills you get from it are so, so different to those you get from your studies. Although, it is important to note that you aren't spoon-fed anything, so if you don't put in the effort you will fail or have to drop out.
Choose a topic that you are really interested in (I did mine on PGD and genetic engineering of embryos despite going to uni to do Law), because you can always make it relevant to your application. Even if you can't make any links subject-wise, unis tend to love that you can study independently and do so successfully.
I really enjoyed doing mine and saw it as a nice breather from my actual school work - plus, if you really put in the effort, you will be so proud of the end product! :-)