I replaced the front and back stock speakers in my '11 vert. The change of the back speakers wasn't difficult, but also didn't provide a huge improvement. I would recommend to let them stock.
The front door speaker replacement (not the subs) weren't that easy but not a huge problem. The replacement of that speakers was a huge improvment.
The stock subwoofers in the fornt doors are really special. Every speaker is a double coil speaker with low impedance (1.8 Ohm), so that the factory amplifier can be cheap. If you replace the subs you will probably need an additional amp. Also the magnet ist pretty small and has a thread that it can be screwed on the sub housing.
My settings now:
Front: 6x8 3Way TS-A6874R (Pioneer)
Back: 6x8 2WAY KS68 (Kicker)
What settings do you have the head unit on for sound? With the stock speakers, I found myself setting it to "driver's seat" with the bass at neutral and treble to about 2+. I have now changed the settings to bass 1+, treble 5+ and in the "all seats" setting. I have only replaced the 6x8s with the TS-A6874Rs so far.