I will give you my thoughts for what it is worth but so you can put my experience into context my daytime job is in IT so I am used to working with things that are technical but I have never had any experience with programming a Pronto up until I purchased mine about 2 months ago.
Question #1
I would say no you do not need to be a PHD however you must be farmilliar and comfortable with computers and the windows operating system look and feel. If you consider yourself moderately technical then you can do this. However I caution you depending on how elaborate you want to make your configuration and the number of devices you can invest anywhere from 50 to 500 hours for a working config. This is one thing where what you put into it directly relates to what you will get out of it.
If you do go ahead and purchase the TSU3000 I would highly recommedn purchasing a user guide devloped by a Pronto user. It is available over the internet at
www.prontowizard.com. I don't work for this guy or get any comission I am just someone who bought it and would highly recommend it to anyone who want's to do their own programming. It explaines things much better than the paultry user guide and online help that comes with the unit from Philips. It costs around $20 US and in my opinion is well worth the money.
I personally have spent about 100 hours now and have a very good activity based first version with macro's.
Question 3
I do have the RFX-6000 and I am experiencing an issue with it and my DVD player. I can control all my other devices through the RFX-6000 except this one. Not sure why. I have spoken to an installer locally as I have given up trying to fix it myself and he said he trys to stay away from the RFX-6000 if at all possible as he has found them finicky and he recommends to use an IR Repeater instead if this can be accomodated in the setup. I am sure if you get comments from others the will praise the RFX-6000 and say it worked flawlessly for them. This was just my experience. Chances are if i had a different DVD player I would be saying the same thing. For me close but no cigar.
Question 4
The only anomolies I have experience are the occasional lockup requiring a reset of the device and the dissappearance of the occasional Icon from my config file. Neither earth shattering issues and as long as you back up your config often especially when you are modifying it this is a minor nusance.
As far as the latest software it all depends, timing is everything if Philips just happens to launch a new version of the editor and firmware and you get one that is already in the chanel you may have to upgrade. Mine was up-to-date when I got it howeve like anything with computers assume everything is out of date when you receive it and always check remotecentral.com or
www.pronto.philips.com to ensure you have the latest and greatest firmware/editor before beginning.
P.S. I would highly recommend the charging cradle it makes it so much more convenient to keep your unit charged especially when doing programming as downloading chews up batteries quite quickly I am told.
Good luck in your decision making.