Honestly I'm so tired of hearing about how people wish everything could be more like Batman Begins/Dark Knight.
Star Wars should have been more like Dark Knight.
G.I.Joe should have been more like Dark Knight.
Transformers should have been more like Dark Knight.
Enough, seriously
Dark Knight works great for Batman because its what Batman has always been. A dark, brooding superhero with twisted, bizarre villians.
That won't work for these other franchises because it moves to far away from the original sources, which is what any franchise should be aiming for.
The Bay films have brought Transformers to a mainstream audience to the point that everyone now knows who Bumblebee and Optimus Prime are. Thats gotta be a good thing, even if some of the cool kids don't want to share their franchise
And they made a ton of money for Hasbro which should get poured into making cool new toys and such.
All and all its mostly positive at this point. Time will tell if the Bay movies have a positive or negative impact long term.
Frankly the success of these films mean there is a chance that we'll eventually see a re-invented version in the future, just like happened with Batman.