Assuming by "Flash" you mean "symbol animation", it's inherently more limited to real animation and will always look worse and less fluent. It's not horrible, but it can't do things that real animation can only dream of, it's the other way around to me.
If by Flash, you're just talking about the program, yeah, you can do a lot with it and make really great animation. Anything you can do with traditional cels, you can do with Flash.
I'd even go so far as to say that symbols can be used as an effective tool for certain elements and stuff and make the objects better, but they're going to be less fluent overall unless you only use them rarely. Animation always looks better when it's drawn frame-by-frame. It allows for more fluidity and expression.
MLP looks alright for symbol animation, but I think it's far inferior to what real animation can do. I definitely prefer to see something somebody actually drew frame-by-frame to seeing copies of drawings repeated over and over. No offense to symbol animators or anything, though, it still can look alright, I just don't think it can ever look as good as full animation.