As I am eligible to do MS- MIS being Master degree (M.C.A) qualified …?
You are eligible, but getting MS in MIS will not necessarily help you get into leadership roles. Typically, if you want to pursue leadership roles, MBA is the preferrred degree. Think about it ?
Is it getting any problem with US consulate people while I am attending the interview for F1 …?
Getting Visa is a very relative thing, it depends on many factors. You have to be confident and ensure all goes well. It is hard to predict.
Which Unversities/Schools wave off the duration of the course by considering 4 years of work exp…?
There are many schools that offer. You need to do your own research. You need to think about your passion and then decide on what will help you in career and select schools.
Which unversities are recommendable to get admission, will not make any issues while chaning the status from F1 to H1 after completing the course…?
As long as you go to a decent school, you should be fine. It should not matter.
As you will spending good amount of money and time, you need to be clear on your goal and do it the right way. Talk to few people, make an informed decision. We have many articles under study in USA section, read them to get some idea.