I had the same thoughts, but let me tell you my experience...
I just bought my Phantom 2 last week and had it shipped to my house. So BRAND new, out of the box, all updates are already installed on my Phantom 2, so I did not need to do anything to the Phantom 2 out of the box.
The TX is a different story, I fired up the RC Assistant and noticed that my version was one behind the latest. I DID not update to the latest just yet, because it mainly had to do with the gimbal, which I did not attach till later.. So, out of the box, your new Phantom 2 will be ready to fly. I did a compass calibration and let it find the GPS signals, and took it up. Had NO issues!!
Now, here comes the fun part!! After flying it for two days, I managed to break only one prop!! :lol: Anyway, I felt pretty secure in my flying skills. I could land it, without tipping over... a big plus for me..

. So I decided to put on the gimbal. After attaching the gimbal, I then noticed that when I ran the "Phantom Assistant", that now the gimbal showed up and it, was upgraded to the latest firmware as well. So, still, the only thing off, was my TX. I followed the instructions on how to update the TX and it all went well. Here is the part that messed me up..
It was time to calibrate the gimbal. The gimbal uses the "X1" channel, and when I launched the "RC Assistant", and moved the gimbal level on the back of my TX, I noticed that the X1 slider on the screen was not moving! Great.. what did I do wrong?? I messed around with the RC Assistant and the Phantom Assistant trying to figure out, why when I moved the gimbal lever on the TX, the X1 would not move within the RC Assistant.. Here is what I found out after a little research.
Some of the units shipped by DJI have a bent "variable resistor" within the TX. I read this on a few forums and found a youtube video explaining this. After opening up my TX, I noticed that mine was bent down as well. I followed the instructions on this video and now my gimbal is working properly.
http://www.youtube.com/watch?v=UJLIHm2m90E
You might have a perfectly fine, TX, and will not have this problem.
(Remember, when calibrating the X1 channel, the little arrows would not even move on screen for me!). But if you do suspect a bad TX, follow the above video, or contact your dealer and have them replace your unit or repair it.
So, what did I learn. All the updates worked fine on my new Phantom 2. It came out of the box with the current updates, all but the TX. I went ahead and updated the TX and it did not have any issues. I hope this help your fears. I'm enjoying the heck out of this thing, and now that I came move the gimbal on the Phantom 2, up and down, I'm ready to start taking some video.. Happy flying guys.. And let me know if you have any questions.
Mike