Yeah I think the SNES version rules over the DOS one, but that's just me. I have played both extensively and I've come up with a good comparison of the major details here...
SUBJECT | DOS | SNES
COPY PROTECTION
DOS: Refer to the manual every time you played a new game
SNES: No copy protection... you already bought the cartridge!
STORY
DOS: No real storyline
SNES: A goddess comes to you in a dream and gives you the power to lead your tribe to glory in 6,000 years.
MUSIC
DOS: No ingame music other than when meeting leaders
SNES: Background music that fit each era: ancient (4000BC-1AD), awakening (1AD-1000AD), middle ages (1000AD-2000AD), and future (2000AD). Different musics for leaders, city management screen, terrain info screen, and technologies screen.
CIVILOPEDIA
DOS: Extensive entries that presented a bit of history to accompany the in-game benefits
SNES: Just a few lines of text for each improvement telling you its function
TEXT
DOS: Longer names (I dont rememebr how long)
SNES: City names, player names, and even menu options and technology names were limited to 10 characters
The DOS game's technology ELECTRICITY is called TELEVISION in the SNES version.
GRAPHICS/COLORS
DOS: 256-colors on VGA, 16 on EGA
SNES: Not sure how many colors the SNES version had, but they were more advanced than the DOS ones
TRIBE/CIV NAMES
DOS: Name your tribe/civ and leader
SNES: Name your leader
SAVE GAMES:
DOS: 4 save slots
SNES: 1 save slot
ACTIONS/COMMANDS
DOS: Keyboard or menus
SNES: All menus, but there were some "hotkey" buttons.
I would say that new players would find the keyboard easier but once you get used to the menus it was actually faster