You'll need a good lift to run 35's on 2.5. AEV or Teraflex.
The wheels you'll need are the average 4.5 back spacing. AEV wheels are a 5.25 offset. It's a better scrub rate and works best with the AEV lifts. (We're about to open a whole can of worms here Mo-Fo) haha.
Over all more auto jeeps are sold. The manual (23 S, C, B, R, G) is still very popular but not as valuable as the 24S 24C etc... In resale or trade. Just like resale of a rubicon or S package (power).
Also FYI,... The auto is more powerful and fuel efficient then the manual trans. Here's a list of what I've rand over the last few years.
2012 current own auto
1995 current own auto
1945 current own 3 speed manual
1995 5 speed
And I wheeled and daily drove them all.