Uhhhh, a hot topic
Let me start of by saying that I love the current white dialogs
We styled the app dialogs to look like something that belongs to the GTK application - this was a personal achilles heel. I felt like there was a lot of resistance against this design decision (maybe there still is?), but I really think the current design ties the dialog and the application together nicely having tried it in the real for some time.
The original application dialogs looked good too, much similar to the shell dialogs now, they just looked, as you say, ailien coming from an application.
Here’s a quote from the discussion:
…even if it’s a good idea to distinguish app dialogs vs. system dialogs, there are many more coherent ways to do it than changing the shape and size and layout and colour of the buttons all at once! Having a difference in all those things at once is likely to make users think that they were designed by different people who weren’t communicating.
This battle (I’m using the word in the most friend possible way) I lost, and I’m okay with that. As much as I would like to see them (app and shell dialogs) styles more alike, the current shell design look really good, so if they have to be different, this looks good.
The top bars would give the impression that this is coming from an application and not the shell. @didrocks mentioned here that a distinction is wanted.
Changing the roundness and button style would be another way to make them look more similar, but it looks like something is missing: (or maybe I’ve just gotten used to the current design)