I use Lightroom 4 for 99% of my work. I use Elements 9 for panoramas, but that's about it. I too thought LR was very confusing at first. I ended up buying a book about it, I think from Scott Kelby, and it walked me through the important things. Great resource!
Aperture is being discontinued by Apple, so no new updates will be coming. I tried it before I went with LR and thought LR worked better for me.
Also, you can still get LR as a stand alone, which will cost you less over time, but won't get you the extras, like being able to use it on an iPad.
If I can dig up the Kelby book, you're welcome to borrow it if you want.