If you were buying an 06 and planning on upgrading the factory radio and speakers for better sound, would you rather start with the non-JBL system with 6 speakers or the premium JBL system with 9 speakers? If you'd prefer the premium system, what do you think you gain from starting with that?
When I test drove a 2005 with the regular 6 speaker system it sounded muddly (to be kind.) My 2006 with 9 speakers is a totally different animal. It honestly sounds good to excellent.
If you are going to change out the radio anyway, why pay for a more expensive one that you don't plan on using? But either way, to help with your decision, with the JBL setup, you can't really use the HU without the JBL ampm, as the volume, balance, fade, EQ is handled by the amp. The HU puts out fixed level balanced differential outputs to the amp.