There were a few watershed years for the Wagoneer.
The first was 1965, where the original 230 cid OHC and Borg-Warner automatic were abandoned for more conventional components. Pre-65 cars are for collectors only. From '65 on, the Wagoneer got the TH400 automatic, or one of several Borg-Warner manual transmissions. Most Wagoneers out there are automatics.
From '65 through '70, the cars stayed mostly the same except for changing from the AMC 327 V8 to the Buick 350 in 1968. Sometime around '68, the weaker nutted two-piece D44 rear axle was replaced by a flanged 1-piece axle. Significant upgrade.
In '71, following the purchase of Jeep from Kaiser Corp by AMC, AMC started using the 304 and 360 AMC V8s. The 360 continued to the end of the run in 1991. Some were built with the 401 V8 or the 258 inline 6, but most were 360s. The 304 was dropped for the Wagoneer in 1972.
In 1973, the revolutionary Borg-Warner Quadratrac transfer case (BW1305 and BW1339, with and without low range) were introduced. These have very significant parts issues today. They wear out chains in roughly 60K-100K miles, and the USA-made chains are gone. Crown supplies import chains of unproven quality (early import chains were junk). Virtually all automatic cars '74-79 got the Quadratrac. With the loss of the USA chains (Morse), the part-time conversion is NLA, I believe. Read the Jubilee Jeeps page before you consider a Quadratrac -
http://www.jubileejeeps.org/quadratrac/
In 1974, the Wagoneers and J-10 trucks went to 6-lug wheels and a new front axle, the open knuckle Dana 44 with disk brakes. This is a major upgrade. Prior to 1974, the front axle was either a Dana 27 (through 69ish) or Dana 30 closed-knuckle axle. The open knuckle axles have a tighter turning radius, require less maintenance, are stronger, and the D44 is a big upgrade from the D30.
The next watershed year was 1980, where the TH400 was dropped and the Chrysler TF727 was fitted, along with one of several aluminum case chain drive new Process transfer cases (NP208, NP219, NP228, NP229). The front driveshaft drop changed from passenger side to driver side. Changes from here to the end of the run were mostly cosmetic or emissions related. Jeep started putting the AMC Corporate rear axle in these cars (M23), but it's not the same as the weak M20 axle that came in CJs - stronger tubes and 1-piece axles, basically equivalent to a flanged Dana 44.
If I had to choose, I'd choose a 1974 through 1979 model with a manual transmission. Manual transmission cars did not get the Quadratrac, instead getting the venerable Dana 20 gear-driven case.
Starting in 1977, the Wagoneer (model 15) went upscale and was split from the down-market 4-door Cherokee (model 18). Don't overlook the Cherokees from this era... they came in 2-door narrow track (16), 2-door wide track (17) and 4-door narrow track variants. Almost all Wagoneers after 1976 were V8/Automatic/full-time with all the bells and whistles.
I may not have gotten all the years exactly right - you can check the drivetrain database on IFSJA if you need more details
http://www.ifsja.org/tech/figures/db.html