That is a big question with a lot to look into. However, I think we can hammer out some generalizations.
When you say "old" Japan, what is "old?" 1100's, 1500's, 1800's? I'm not familiar with ancient gender relations, but the example you site of a man holding life and death control over his wife is, I believe, something of an overblown story. Sure, men probably did kill their wives for a variety of reasons and some probably even got away with it, but a few extreme examples does not make an accurate picture of general gender relations.
It seems, from what I can remember reading - sorry I don't have the sources with me - but country women or women of low-ranking nobles/
samurai enjoyed greater freedom and voice both within and without the home than aristocratic women. Like in other cultures, high ranking families often married off their daughters in political unions and other such property-like exchanges. Women were in no way equal as we think of it today, but then society was not equal for men either. Women and men had spheres where they conducted and enjoyed almost complete control. Women might not be found in seats of power (though there are a few notable exceptions and women who ruled form behind the scenes), but inside the home, often they had the last or equal word in domestic matters. Country women could divorce and run away and there is little a husband cound do about it. They also seemed to have had almost full control of the reproductive rate of the family, and abortion was not uncommon, depending on the studies you read.
Weather or not we should think of them as being viewed as property is not within my power to say. However, it would suspect that the more important women were to the basic survival of the family unit, like on a farm, the greater freedom/leeway they could expect (thought I could be way off-base;just working from my often flawed memory - corrections encouraged...).
Your second assumption, that women hold the purse strings at home, is more accurate, but changing slowly if my young married friends and wife are any gauge. A salaried worker would often give his pay directly to his wife who would pay out an allowance and manage most of the day-to-day finances. Large purchases like cars, homes, big vacations would of course be made together, but the wife would probably have a better understanding of the household finances and the fesability of large purchases.
I do not think this is an unnatural arrangement (not that you were implying it was otherwise). With a husband at work so often and for so long, when could he find time to keep abreast of family finances on a minute level? It is not his job to budget for food each month and find what is on sale at the stores. Why wouldn't that job fall naturally to the member of the family in the best position to manage it?
As for your last question, not being a trained or well-read in trends of gender relations or an anthropologist, I will leave it to others to flesh out. However, when looking at trends in Japan from a western standpoint (and a good deal of subconscience value-judgement does go on when talking about such topics), societies tends to change slower than their political or economic components. Japan modernized and attempted to change in 40 years what took the west more then 400. Political structures can change overnight or over a few years, social structures tend to move a great deal slower.
PS, welcome to JREF and enjoy the fourms