From what I (vaguely) remember, the reasons behind moves like Dolphin were that they felt the integrated Konqueror was a mistake. It certainly made for hard maintenance, the integration system often broke after small changes; and I can imagine security was an issue. Microsoft had made a similar choice in Windows 98/2000/XP, and went through a similar backtracking after XPsp2.
Also, they were trying to move the system to Qt4, which was a big task. Breaking things up probably seemed logical. Add a bit of classic FOSS bugfix-is-boring-let's-rewrite, and voilà...
Of course, in MS’s case the backtracking happened primarily because after years of court battle and endless millions of dollars they were told they’re very much not allowed to deeply integrate the browser to the OS. There never was any technical or usability merit in marrying the two Explorers, it was 100% Microsoft’s attempt to own the web.
Also, they were trying to move the system to Qt4, which was a big task. Breaking things up probably seemed logical. Add a bit of classic FOSS bugfix-is-boring-let's-rewrite, and voilà...