I'm all for it...
Technology is only going to get better and easier to use. The advantage is that you can spend your time working on more important aspects of the shot... the lighting, the look, the movement, or just simply being able to use more of it, allowing you to make movies like Transformers where the stars aren't even real things.
But the downside is that it becomes so easy to use, everybody starts using it everywhere. Why build a model of a city to blow up when you could just CGI it? Why use a fake gun with blanks when you could just CGI it?
True, this is bad for Hollywood but I don't think it's bad for movies on a whole.
Look at your examples again. It's not the CGI that makes them so good, it's the quality of the movie that makes it so good. Those independent film makers really cared about what they were making. They want to see a Portal movie... a real one... not some fucked up Hollywood adaptation where they change the lead character to an infected human and the portal gun to a transportation device. A real portal movie... about a nameless female specimen shooting portals into walls
Before, this was impossible. You couldn't do it without CGI and the technology behind CGI was too difficult to use. But now... now anyone can do it... and anyone will. So if you want to make a Portal movie, make it. But you better do a damn good job because there are a hundred other people out there just like you who are also making a Portal movie. And if they're not filming one now, they'll probably start after they see yours.
I think it actually improves movies. Soon, Hollywood will have no choice but to compete with independent filmmakers... so their bullshit 'fuck up the story' routine will no longer work. Why would you pay $30.00 to go to the movies to see a bunch of over payed fuck heads ruin your favorite video game when you could pay $10.00 to an actual fan of the game and see a better film shot with the same HD standards and CGI technology as the professionals.
In short, it builds competition, which drives a better product.