When I was a kid, one of the things on which I spent a fair amount of time was trying to figure out how to make a Lego vehicle with independent front suspension (and steering). Nowadays, they have specialized pieces that have effectively solved that problem.
I don't know whether I ever came up with a decent solution back then, but I do know that trying to come up with one was an excellent exercise, one that I probably would never have embarked on if I'd had the pieces they make today.
edit: grammar fix
So your endeavour is replaced by others. Your logic could easily be used to rail against using calculators rather than slide rules or to rail against all Lego in favor of Erector sets, etc.
As others have stated, Lego was in trouble before adopting the franchise sets. Would it be better if Lego was 'pure,' but out of business? It's not like they removed the ability to do what you're talking about, they just added new things. You could easily limit yourself, or your children, from using the new things.
2. You can go to places like bricklink.com to buy almost any block or set that you want.
3. Branded sets usually mean more specialized pieces which only increase the source material you have to draw from when building things.
4. Lego also puts out stuff like this: http://www.eurobricks.com/forum/index.php?showtopic=67132. Highly specialized pieces that aren't tied to a brand.
When I was a kid I would have been in heaven if they had all of the sets out there today. Buying a Harry Potter set wouldn't have meant that I can only play Harry Potter[1]. It would have meant that I had more legos to combine in other ways with the rest of my parts (all sets ended up broken down and stored in a huge bin of Legos). I realize that ultra-specialized pieces like 3-CPO or R2D2 minifigs can't really be reused elsewhere, but most specialized pieces tend to be pretty generic (e.g. Harry Potter wands don't have to only be used with Harry Potter).
[1]: Example, I recently saw a Harry Potter set that used a combination of a translucent 1x1 brick and brown stud to create 'potion bottles.' It's a pretty generic idea that translates elsewhere.