Asalamu Alykum Ali Ashkar
You asked
Then can we conclude that polygyny was restricted to not marrying two sisters together and other than these cases Quran allowed polygyny?
As hard as it may seem to accept for some, and some may even try to give exceptions on when a man can partake in such a marriages the simple answer to your question is yes. It seems like it always has been accepted by the Lord from the people of old and the people of today.
can we understand then the case in 4:3 as using polygyny(which was prevelant in muslim society) to solve the problem of men not willing to marry slave girls and widows(widows with reference to "yatama alnnisai"-4:127) in those days?
God knows best if that was the reason why or part of the reason. However that very well could be a positive thing for sure for the orphan women, slaves, and widows who wished to get married in a society of old which accepted polygyny and such marriages were considered to be
"normal" by men and women. One can always surmise reasons and factors like that due to wars that there may always be more women that maybe desiring to get married and not enough men. God knows best why.
At the end, there is support from the Quran that polygyny is acceptable which also one finds from the Quran that there is responsibilities that go along with it. Also it seems that the Quran does not encourages nor discourages multiple marriages.
A couple related articles are
Peace
MARRYING FOUR WIVES IN ISLAM
http://quransmessage.com/articles/four%20wives%20FM3.htmCritique: Marrying 4 wives in Islam
http://quransmessage.com/forum/index.php?topic=1090.0