There are two things preventing them from doing that:

1. They'd have to reach out and agree with each and every mod maker if it is ok to use their high res patch and whatever in the release. Many of them probably want money for their work being used in a commercial (re-)release, so GOG probably figures yeah no.

Some games come with such optional fixes though, if the original game is quite buggy without the fix. Like Gothic 3 and Deus Ex, I think.

2. I usually want to play the old games as they were originally intended, so GOG has no permission from me to integrate such widescreen patches etc. If the original game ran on 4:3 aspect ratio, then that is how it shall be delivered to me (and everyone else).

I am not going to change my mind about this, and GOG can't do anything until I do.

I still do that for some games. In fact that one of the reasons I made this thread. Do or do I not use Widescreen patches? Some, (like the one for Splinter Cell) increase the FOV to such high levels that's it's clear the game wasn't meant for it. While others such as the one I used for Sands of Time are able to preserve not only the FOV but also the aspect ratio of the games cut scenes. In my opinion nemesis makes the best fixes http://ps2wide.net/pc.html#popst they stay rather pure to the game and have next to no side affects

This. When I buy an old game I always want to play it as they were originally intended.

Deus Ex still uses 4:3 and low rez until it's it's been modded but really...! Why? why is a problem if widescreen settings are made available in the options menu. One example of a game heavily modded from the original that GOG is selling is System Shock 2

That's a good point.

Why would you want to change your widescreen resolution once you've set it?

Widescreen fixes aren't just something you can pull from a hat. They have to be skillfully made and designed, as otherwise you end up stretching the picture like someone watching an old show on a new TV.

What he means is that everyone's screen is different. Mine is 2560x1440 so 1080p looks blurry on my screen and if 1440p was defaulted and you tried to use it on a 1080p screen you'd run into problems

Sure, but most (I'm sure there are exceptions) widescreen fixes let you set your own (native) widescreen resolution. The only issue I've ever had with widescreen fixes is a stretched HUD. And I'd rather play 4:3 than have anything stretched.

Some widescreen fixes are rubbish, Nemesis makes really good ones. But I still think you have to enter the rez in manually. But there's no weird stretching or FOV nonsense with his fixes.

Ok, let's say we're talking about 3D games...
(I know, widescreen fixes exist for some 2D games, like the Infinity engine games. But in general, they're exceptions)
Maybe GOG could adapt the widescreen fixes so that the desktop resolution gets automatically set. That would require no 'advanced' knowledge from the end user. But these days most people have screens with a relative high DPI.
e.g. the original Neverwinter Nights: setting it to 1920x1080 on a 24" screen makes the HUD/UI pretty small.
I guess the question is... could GOG write an installation routine that sets an "ideal" widescreen resolution based on DPI?

I would suggest sometime much simpler. Download widescreen patches from reputable moders such as Nemesis or any of the other widescreen patch sides (they typically have these things in bulk) Test them and see how well they work. If they work well with without any nonsense from the user and are able to preserve aspect and FOV then just use those. If it's anything more then that. Add a link or something.

I also want to bring to peoples attention that all Dark Engine games are modded to work with widescreen patches. This includes System Shock 2, Thief 1 & 2