Well there is a few issues with the sound system, wiring up an after market HU is a hassle, the wiring kits are usually crap and there have been issues with a similar to a turbo spooling noise coming through the speakers when you are driving along which is super cool if you like to think your IS is boosted.... a few audio specialist workshops will actually open up the factory amp and can wire it up to accept an aftermarket unit, like mine had done to it, it sounds absolutely mint and alot more powerful now.
The speakers that are in the car standard have different sized mounts, so 6x9's wont exactly just drop straight in there, they are also wired to an amp that is to the left of the glovebox which makes changing the head unit a hassle, if you are going for a screen which i would recomend, you will find that any dash fascia kit you look at wont match up with the rest of your dash with regards to texture and colour, so if you are looking for perfection you should be prepared to fork out an extra $450 to get the dash kit molded, sanded and painted, it will probably only run you around $300 if you just want them to sand and paint it. then you could always go DIY and save.. but paint matching is a problem..
the issue i had when i took mine to the shop to get it all put in, the careless *BLEEP*s practically shoehorned everything in and out.. so they really made a mess of my dash, so tell them to mask up around the head unit before they work on it.. the whole dash, air vents and centre console in my car was replaced at the workshops expense, it ran them over $4500....
if you get a decent HU (say.... Alpine IWA-505) with inbuilt cross overs for the small speakers, you can fade all of the low end to the sub and the mids and highs to the speakers and tweeters, the standard speakers go pretty hard and wont distort this way and will last longer.
what i did for mounting my JL amp required my ski pass to be removed and a new wall was put in, the only issue is they ran the cables through the hole in the ski pass... so when you put the arm rest down you can see the wiring... i am yet to fix this...
but what ever you decide to do in the end, good luck and i hope it all works out for ya! :P