Yea I know about this and thought about what the actual impact is.
The Installers only work on XP and later so anything from the XP era should be fine for us.
Windows 98 SE games you are better off buying the original game. GOG.com hacks, mods, patches the games to death and often leaves them broken on old PCs. Tomb Raider II is an example which will not run on a period correct machine. But that games doesn't run well on Windows 8.1 either, so who knows who's to blame.
DOS Games, no big deal as they will continue to use DOSBox with the odd Scumm VM game thrown in.
The main issue I have is the lack of information what they changed to get the game running. Unless you search the forums or ask, they won't tell you if they game uses DOSBox, ScummVM, comes with the installation image or not, uses a wrapper...
GOG.com certainly has changed since the early days with them focusing on MS-DOS games. They quickly figured out that this is a small niche market and expanded and now the site is flooded with indie games, movies, Windows XP games and you need to really dig for the old goodies.
Still, it's another option, another tool in the toolbox of Retro Gaming. Sure it's not perfect and things can get annoying but there will be many releases which are retro friendly such as the many DOSBox based games but also games such as Gabriel Knight or Screamer 2 which come with the full CD image ready to be burnt and played on your Retro Gaming PC.
So I don't worry too much about the negatives and focus on what each distribution platform does well. The biggest complaints seem to come from the Linux Gamers but I believe that Windows XP and later gamers should be fine.