Erny - you make some valid points.
I have only played one or 2 games of WHFB at the height of the 90's GW strangeness and was not that impressed and put off more by the all the GW 'fluff' associated with it. As a primarily historical gamer used to rules and figures being considered separately I found all the GW corporate integration a bit too much. But I agree that's probably not enough exposure to make a really valid comparison.
I always thought that Warhammer was best when the setting was very vague - as in first and - though less so - second edition. From third edition on, it seemed to get more intrusive and fiddly. As an example, hobgoblins in the first and second editions were subject to frenzy. But in the third edition, they were subject to frenzy
if they belonged to the Mourngul tribe and
if they had a portable shrine on the battlefield. That sort of thing was a retrograde step, I think.
Now, the RPG setting was very interesting and absorbing. But I don't think it every quite meshed with the wargame setting. The RPG was much more human-centric, with just a hint of hooves under cultists' robes or scuttling things in the sewers, or prancing beast-creatures in the woods. The garish green orcs and goblins didn't really fit with that at all - and nor did much of the other kitchen-sink wargaming stuff.
The other thing that they did, of course, was to start linking specific models to specific rules to a greater and greater extent. So, rather than just make up your goblin chieftain and give him a name, you would buy a specific hero to lead your army. You could argue that that element had been there from almost the start with the Regiments of Renown, but I think there was a difference between a well-known unit showing up in an otherwise original army and set characters (with specific models and rules) being a commonplace across armies.