Ghorpm: You finished Dune 2 with Atreides? You can congratulate yourself, AFAIR it was the most difficult campaign.
I personally thought Ordos (the green ones) were the most difficult. Maybe this was because their special unit was pretty crap compared to both Atreides' and Harkonnen's special units (meaning the tanks). On paper it sounded good, being able to convert enemy units to your side, but in practice it was quite crap.
What made Atreides especially easy was the bug that (IIRC) if you slowed the game speed all the way down from the options, your special unit (sonic tanks) would shoot at an incredible range, and they could kill enemy tanks long before they got to firing range. On the other hand, if you speeded the game up, your sonic tanks would suddenly get laughably short firing range.
I don't know if they ever fixed that bug. I replayed the game last year or so, with the latest (at least official) patches, and I think the bug was still there. Not sure though.
As for Dune 2000... yeah it was nice, but I liked Starcraft more (as a single-player game, at least). And as many others have voiced the opinion, Emperor was (even) better. I really should replay Emperor at some point, all I can remember is that it left a good taste in my mouth, even though I don't remember that much of the actual game anymore.
While Dune 2000 is a Dune 2 remake and had much better user interface and game engine, I still felt playing it was quite a different experience. So in that sense I don't personally feel Dune 2000 fully replaced Dune 2. Then again, playing Dune 2 nowadays with its poor UI is a feat in itself. Painful micromanagement hell.