Alright, I can't say what's important to you, but some ideas:
1 - Geographical factors. Would you rather study in Auckland or in Dunedin (then possibly Christchurch or Wellington)? Which is closer to home? Is this good or bad? This was pretty much the decider for me - Christchurch is my hometown, so studying in Dunedin meant that I could leave home, but it'd be easy (and cheap) to visit when I wanted. At the same time, lots of Aucklanders choose to come to Otago specifically to get away from their parents! Other factors include the cities themselves - which one do you like more, practical issues (e.g. rent in Dunedin is a LOT cheaper than rent in Auckland).
2 - The universities as a whole. Which campus do you prefer? Which do you think has the better culture? Where could you study more easily? Personally I love the Otago campus.
3 - Where are your friends going to uni?
4 - The medical schools themselves. Generally Otago and Auckland are pretty similar, but there are some differences, particularly at years 2/3 (where Auckland is a lot more traditional, with lots of lectures and tests, 7-8 papers, and grades, compared to Otago which is more clinical and self-directed - though still a pretty conventional sort of university course).
The vast majority of people I know at Otago chose it over Auckland on the basis of these (and similar) factors. I don't yet think I've personally met anyone who chose Otago specifically because they thought it would be easier to get into med here. Ultimately you're at med school for 6 years, and just thinking of admissions at this stage (while perfectly understandable) runs the risk of becoming short-sighted.