The options depend on the relief that you seek.
Keeping in mind the time that has passed in this matter, I would suggest the following:
1. If your sister wishes to divorce, she has ample grounds in her favour. Further, she may also claim maintenance from the husband. The complaints already filed will work in her favour.
2. If your sister does not want a divorce but just maintenance for the time being, she has reasonable grounds to do so as well. Though it will have to be proved that they have not been living apart through mutual consent. Again, the complaints should work in her favour.
3. If your sister wishes to pursue a case of domestic violence, the major issue that might work against her favour is the lapse of time.
I would advice that option no.1 would seem most favourable keeping in mind the facts provided.
Alternatively, if your sister is looking at an amicable solution, then your sister may also forward her grievances to the National Commission for Women, Delhi. They will take up the matter further and do what is necessary. This option would be most cost effective.