The key is whether you have to connect or not. On our last flights on American we went RT San Diego-Buffalo, and one leg was on American Eagle.
Our flight there arrived about three hours late, after a connection delay, and that was bad enough.
Our flight home, which was due to depart Buffalo on AE at 6:00 PM was reported to be on time when we left for the airport. When we arrived the monitor still said on time. To make a long story short, they kept delaying, and we left late enough that instead of getting to San Diego on the final flight at 10:30 PM as scheduled, we arrived home at 4:45 AM. And just to add insult to injury, the ONE bathroom on the small American Eagle flight was out of service!
I have been an American frequent flier for years, and will still fly using my miles, but when I am paying these days, I prefer Continental.