Both cities are in the top 10 in the world (according to Mercer Consulting anyway) so it typically comes down to mild preferences, career opportunities, personal hobbies, friends/family
i.e. you prefer
- large anonymous city versus village-city
- beaches (swimming) versus hills (mountain biking) on your doorstep
- warm versus cool climate
- warm houses versus cold uninsulated wooden houses
- humidity versus windy
- greater range of cheaper airfares / shopping / food vs greater concentration of food outlets in CBD
Auckland is big enough, area wise, that you can live in the type of area that suits your outlook on life...e.g. rural views or parks in the middle of a city (One Tree Hill), sea views, beaches (St Heliers, Kohimarama, Mission Bay, Takapuna), shopping (Newmarket), gay suburbia (Ponsonby, Grey Lynn), medical/blue chip (Remuera).
Of course the trick is to be able to find work or a source of income "close" to your favourite suburb -- and this can be difficult.
Nevertheless there are places in many cool suburbs close to easy motorway travelling, or express busways, or train stations which can make travelling a cinch, if your work is in the right place.
Wellington is very handy, and especially if you are in the city suburbs (e.g. Mt Victoria, Kelburn) i.e. not Churton Park, Tawa, Porirua, Hutt) can be more accessible to work and CBD than Auckland. (But if you have health issues, note that there are many houses in Wellington that are uninsulated, or in areas with lots of pollen, or have lots of stairs to climb.)
Being smaller, Wellington is more "provincial" in the sense that you are about two-three degrees of separation from another person in the street. So this factors into work and career advancement --- if your industry is more likely to be parochial with the typical insular and xenophobic NZ-style management, Wellington might not be the place, if your focus is on on corporate career development. Of course Wellington is the place to be, if focus is on government/public sector.
Don't know what private business enterprise environment is like here.
Cheers!