Honestly, I think it was one of DC's worst cross-overs ever. Some of the tie-ins were pretty good, and I liked the premise of the Manhunter infiltrating the heroes lives in many levels (which years later would be aped by Bendis in his not-so-original "Who can you trust?" Secret Invasion), however, IMHO, with few exceptions, they chickened out in most cases and gave us irrelevant "infiltrators", and, in some cases, they even ruined good characters with good story potential just to hammer them into a "shock reveal." I also thought that the Manhunter Cult had A LOT more potential as a threat then they were actually shown to be. The main series itself was merely a teaser for the meat of the story in the tie-ins, and I do think a past its prime team of Steve Englehart and Joe Stanton did not have the juice to carry on a company wide event (in which their work would be put under a microscope in comparission with all the new blood and talent then working at DC). While I loved the idea of the DCU against the Manhunter Cult, I have to say the "Search for the Chosen" part of the story really didn't do anything for me. The characters were, IMHO, bland, boring and stereotypical (though probably exactly what you'd expect to find in more "diversity oriented modern books", so I guess, in that aspect, they were ahead of their times), and I really didn't care much for them nor for their "super-heroic" identities. All in all, IMHO, while I do think Millenium had tons of potential, I have to say I found the execution extremely lacking. Sorry if that's not the feedback people were looking for.
Peace