Have not owned Alden boots for that long however have done a several multi mile walks in the CXL indies(cork), NST boot(commando), & J Crew shell Captoe(leather sole) and my other boots are AE(10), Vass(1), Viberg(2)...out of all of them the AE in all soles is most comfortable to me on longer walks. My guess is that the AE are lighter and more importantly comes in tons of widths and goes up to big sizes without having to jump through hoops to get. So I guess fit is really the key factor.
I am loving the Alden's I have though and wish it was not a pain in the arss to get them in my size in the special makeups from the retailers. Looking forward to adding more!
That's interesting as I have been frustrated with AEs widths lately. Alden stocks all their factory shoes in a ton of widths, check AldenShoe.com. They don't typically skip widths. If they don't have one in stock, they will immediately make you a pair. I did this with both my 975s and 9751s. Of course immediate is 18 weeks... AE has not been making C widths on many of their newer lasts, which has forced me to be creative, if you actually look into it, AE actually has a sparse width array and frequently skips widths, but they are readily visible on their site. One frustration on Alden special makeups is they limit runs to three widths for some unknown reason. They just do. Also, as you alluded to, their vendor special makeups are a pain to figure out.
In terms of comfort, they all really come out equal to me if they fit properly, although rubber soles like the Commando (Mini-Lug in AE) or the Neocork can help insulate shock some.