This thread needs a visual comparison too.
Which one is better? Neither, they are equal. It just depends on what features you want in a bass.
Construction wise, I'd say they are equal as far as the quality of the build.
Both are 35" scale but the Millennium feels shorter for some reason. 21 frets (Mil) vs 24 frets (Cir) might be the reason. Both are nice but to me the Millennium is more comfortable.
The Millennium has a string retainer and the Cirrus has an angled headstock. (probably give the edge to the Cirrus there.)
The Millennium is bolt on and the Cirrus is neck through. (Toss up depending on what you like)
The Millennium has a shallow neck (front to back) and the Cirrus is somewhat chunky. They are both nice but I prefer the Millennium's narrow neck.
The hardware is similar except some folks have complained about the rubber knobs on the Cirrus (doesn't bother me)
The bridge (IMO) is far better on the Millennium (Hipshot type A). It's much easier to work with when setting up string height, spacing, and intonation. The Cirrus bridge is a giant PAIN to work with. I don't like the loose string saddles that flop around and fall out if you're not careful. Also the Millennium offers both string through body and bridge, while the Cirrus is string through bridge only. String spacing on both basses is the same btw.
The edge again goes to the Millennium for trussrod access. The Cirrus has the commonly used headstock trussrod access, while the Millennium (because of the bolt on neck) has an easy to access wheel at the body end of the neck. The Millennium is by far the easiest bass I've owned to do a setup on.
Ok, but what about tone you say?
While they both have a somewhat similar tone, (you can tell they are from the same Peavey family) they both have their individual personalities. To me, the sweepable 3 band EQ on the Millennium vs. the fixed 3 band EQ on the Cirrus is a wash. I leave both basses flat and adjust EQ on my amp. If having a sweepable midrange is important, Peavey will sell you the Millennium preamp to put in a Cirrus. I personaly wouldn't bother but that's just me.
The Cirrus would probably be the choice of most folks (just guessing here) because it's two Humbucker soapbar type pickups sounds sort of like a hi-fi active Jazz bass especially when the bridge pickup is favored. Nice focused tone all the way down to low B. Some have said that the Cirrus is lacking in low end but I can't imaging anyone not being able to add enough low end with the active EQ.
The Millennium on the other hand has a J/ neck pickup and a M/M pickup at the bridge. Even though the Millennium also has an 18v preamp, (IMO) it is more traditional sounding than the Cirrus. Think Musicman meets P bass with emphasis on low, low mid growl. IMO opinion both basses have a nice singing high end (not harsh).
So I'd say everything is pretty even with these two basses. I'm playing my Cirrus more these days because I'm primarily playing in church and the polite tones of the Cirrus seem to be a good fit. I think the Cirrus would be best for R&B also. For classic rock, modern country, blues, I'd probably grab the Millennium.
I've considered selling my last Millennium 5 (I used to own two) and get a 2nd Cirrus, because I am having a little problem switching back and forth between the two neck profiles. But everytime I do, I get it out and play it awhile and decide too keep it. Besides that, the resale on the Millennium is so bad that I wouldn't be able to get near the money I'd need for a Cirrus or even get a bass near as good as the Millennium for the money I could sell it for.