I find it humorously ironic that we are told not to modify the files of an open source project. What's next, WordPress shipped only in encrypted binaries?
If you're working with a modified version, then you cannot be expected for the development team to take your unknown modifications into consideration. This has nothing to do with it being open source or not, if you want support, you're not going to get much of it if you're running something entirely different than that which is supported.
Sure, modifying core files is not preferable, but there's absolutely no reason to make users risk overwriting customized files if the upgrade in concern didn't even modify the file!
No file is an island. Changes in one place will have effects elsewhere. This is one program, not a collection of loosely interrelated ones.
That's exactly the elitist attitude that frustrates users and sends them to Microsoft. Do not add excess complexity to products, especially when it's so easy to deliver a simpler method ala Gallery2.
"Sends them to Microsoft"? Are you serious? This is not a war between "us" and "them". Microsoft offers perfectly legitimate services as well. And yes, if you can't deal with technical stuff, then yes, you might want to turn to Microsoft products instead.
There's a reason people get paid to be IT Professionals, and thinking that any person off the street can walk up and do the things that people like myself do every day without having to actually learn something is, frankly, insulting.
I'm sorry, but life is full of things you don't understand. Learn, or don't, but don't complain that life shouldn't be that way. I have spent a lot of time in my life to know what I know and to do what I do and yes, I even get paid to do it. And yes, suggesting that that doesn't or shouldn't require technical knowledge is ridiculously stupid. It is not elitist to say that one should have technical knowledge to do technical things.
Deal with it.