I have an 01 and an 05 currently.
My 05 seems quieter to me, and the facelifted interior less chintzy. Just my opinion. I have all new OEM engine mounts in the 01, and the 05 still seems quieter.
I like the Duratec engine in my 05 better than the Zetec in my 01.
I have not had the hard starting issue the 2005 cars supposedly have. Never once has our 05 exhibited any starting issue. Not saying it doesn't exist, just that it has never happened to me.
Ours (05) has right at 99k miles and has a slight tick. I have a new intake manifold sitting on the shelf in my garage awaiting warm weather for installation. I could probably drive it the way it is for a long time, but I'm anal like that, so I'm going to replace it.
I would buy another 05+ wagon in a second. Earlier car...hmm, would have to think about it. Probably. I settled for the 01 even though I would have rather had the later style since stick shift wagons were so hard to find. The 05+ stick wagons seem harder to locate than the earlier cars, and an early stick happened to pop up for sale near me so I grabbed it. Was a right place right time kind of thing.
Lack of a timing belt on the 05+ cars is a bonus in my book. The powerband of my 05 seems better suited for city traffic than my 01. Seems gutsier down low. The Zetec, I feel like I have to rev it out more. Might be in my head.
Other posters are correct that the rear tire wear is an issue. More apparent on my 01 car than my 05. I have new adjustable MOOG rear arms for the 2001 that are also awaiting the nicer weather when I can work on my car in the driveway. Too cold now, and my garage too full of kayaks and bikes and motorcycles to make room for a non urgent repair right now.
My advice would be to buy the newest wagon you can find with the lowest miles and best history. They are all starting to age by this point, so the newer the better in general.
In my area, wagons are hard to come by used. When they do pop up, they sell fast and for a premium over the other body styles. This is what happens when hardly anyone has built a good small wagon for a while. The good used ones get sought after. Most manufacturers moved into crossovers and abandoned small station wagons. As time has gone on, small wagons have become harder and harder to find in good shape, and the ones that are left tend to hold value and or sell quickly. At least in my experience. On the coasts, where wagons may be easier to find, this may be less the case. Manual transmission wagons are like pink unicorns with three legs in these parts, but since you're looking for a slushbox, your search will be much easier.
If Ford sold a new Focus station wagon in the USA, I'd go down this week and buy one. But they don't, so it might be a Subaru or VW for me at some point when the 01 bites it.