I have used CI for some time, and recently started using Phalcon as well, when the future of CI was in doubt. I like both. Phalcon has some advantages over CI, and CI has some advantages over Phalcon. Some major advantages that CI has over Phalcon is that it is more portable and can run an many more server configurations due to Phalcon requiring root access and dependencies. CI is more mature and has been around longer. It's releases are quite stable. CI has more utility classes such as helpers etc which are very useful. CI has better (in terms of readability and navigation) documentation. Phalcon has the advantage of speed, but CI is still fast. Phalcon has better support for auth and ACL. Phalcon has a fast and efficient template system (volt). It's easier to use Phalcon for multi module HMVC apps. Phalcon has a more rapid development program with many more regular updates than CI while not requiring major updates to your code - having said that it looks like development on CI will be accelerating now that it has a more motivated new home. Phalcon has a good asset minification system.
Someone already touched on this, but if speed and performance is your only concern, then you can't get faster than just native PHP! Someone else also hit on the fact that it's not the framework speed you need to worry about, but the hardware you run it on. Hardware is constantly getting cheaper. I have fixed a few slow, overloading sites just by moving them to new hardware - far cheaper than recoding or porting!
Personally I found CI had a faster learning curve. Phalcon took me longer to learn and I found it frustrating trying to find the info I needed from the docs. Phalcon has multiple ways of making DB queries for example, and while that seems like a good thing, it makes it much more complicated. Also it's more difficult in Phalcon to know what is being automatically escaped and secured. On the other hand Phalcon's CSRF system is much nicer than CI's hard coded CSRF error pages that just confuse visitors. Also Phalcon's pagination is quicker and easier to setup. But then again CI's helper classes are very useful and it's DB queries are clear and more flexible.
The bottom line is this. Use which ever one you enjoy coding with most. Both Phalcon and CI are fast. Both are good. Both have advantages over the other. I'm kind of torn between the two at the moment to be honest. Phalcon seems to be good for some jobs, and CI seems to be right for others. Ideally I'd like to see both pulled and merged into PhalconIgniter - now that would be the dog's *****!
