I recently changed the head unit in my coop to an alpine unit which made a whole lot of difference to the sound quality in the car. I would reccomend getting an mdf stealth shelf for the back to mount your speakers onto especially if you go down the sub route. I,ve found that if you match up the RMS values of the amp and speakers then the amount of bass and sound from a set of 6x9" is pretty good.
My old mini had no reer seats just mdf panel 2 x 10" sub and a set of 6x9 running of two amps ( my poor battery) now that was loud.
The standard speakers in the leon doors are pretty good and should be more than capable of handling a decent head unit can throw at them.
From experience make sure you get a good quality amp as some of the cheaper ones are pretty shoddy when you start throwing toones at them and dont be blinded by MAX WATTS etc.
Speaker wise cant see past JBL for the price and performance. I would suggest getting and amp and running a set of 6x9 to start and see what you think after that. Ice is something you can add to as you go untill you get a system you are happy with.
Depends if you want people to see or hear you first.
Hope this helps