Well, there are some objective criteria that can be compared such as housing costs, taxes travel time, etc. That is more or less easy to manage, except the fact that it changes very quickly if you want to live in the center of a big city or 20mn away, if you go to work between 7-9 am or later...(or sooner...)
You know, there is no general rule to say "this canton is better than this one"... I was not saying that Geneva is better than ZH, it is just that depending on what you are looking for, what your plans are, one with a higher tax rate might still be better.
Comparing cantons is also a comparison of subjective feelings you can develop towards a region, a culture and people... For some they feel more comfortable with the latin way of life and French or Italian language while other not. For some the most important thing is to spare taxes on short term and leave CH after 3-5 years. For other, they want to relocate on longer term and get integrated. You don't pay attention to the same criteria if you come on short or long term.
Costs of living is not only housing, it is all the costs you suffer while living, from housing to fuel for your car... those costs are very different from one canton to the other, sometimes from one part of the city to the other and from a city to a land of the same canton! Housing costs in ZH and the low tax cantons are extremely high. Housing costs in Geneva and the region Geneva-Lausanne are extremely high also. Not for tax reasons but because of the lake and lack of housing. Whereas if you chose a house without lake view near lausanne, you might find something at a very affordale price. Same can be said for Aargau. I bet you can find incredible attractive housing prices in Aargau. But can you seriously compare social and nightlife in Aargau with social and nightlife in ZH, ZG and GE? Ridiculous, it depends so much what you want to do... You want to go out, party, have friends, fun, airport, etc? Go to a big city. You don't care of that? Go to Aargau, Lucerne, Neuchâtel, etc.
the best thing I can advise when chosing location apart bringing tax rates and potential tax negotiations and structures, is advising people to come to Switzerland, have a week or 10 days there and go and spend some time at the selected locations. That's only this way that they find out if it suits to their needs or not.
Regarding your question on small businesses, there is as such not a strong supportive tax law for sole proprietorship or small companies. There is no particular (or limited) tax incentives and it does not change a lot from a tax point of view if you go to ZH, GE, NE or anywhere in CH. If you need to negotiate any tax ruling with the tax authority, I would say then go to a tax authority which is reactive. Therefore absolutely avoid VD and GE and go to NE, FR, VS and generally most of the German speaking cantons (even ZH!). But part of that, as long as you fulfill the conditions for a special tax treatment and your request has been well addressed, I don't see any difference from a tax point of view in cantons wishing to attract that kind of business. I would rather tend to say that small cantons are probably more willing to help than the bigger cantons.
From a legal point of view, Switzerland is generally a good place for small businesses, perhaps not as flexible as other locations, but still very easy to manage compared to some locations in Europe.