They had the perfect balance between groove and incredible technique. IMO that's why Portnoy made their music so special. Now that balance is gone.
I respect Jordan Rudess a ton, and his composition skills and technique are out of this world, but I really liked the Moore and even the Sherinian keyboard eras better. Neither were as hyper-technical, but they added more groove. I really love Sherinian's jazzy fills on Lines in the Sand. And Moore's vocal leads and overall atmosphere.
I really don't feel like there's a ton of difference between Portnoy and Mangini though. I honestly think Mangini is a little bit better.
But I don't get emotional about it. It's like comparing apples and oranges, and I simply prefer oranges. I don't think think any album this band has put out is bad, except maybe SC.