I am not sure what the question is. Are you wondering if I think SQL Server will work better or if SQL Server will need the same indexes as MySQL or...?
My opinion about switching database engines is it depends a LOT. There are budgetary constraints, potential application changes, new skill sets as administration of SQL Server is different than MySQL, etc. It is similar and the syntax is similar, but you may need to rewrite some (or all) stored procedures, functions, etc.
Focusing strictly on indexes, SQL Server and MySQL use different database engines so the index strategy for MySQL may not be the right choice for SQL Server. Having not worked with MySQL, I am not certain how their indexes work, but with SQL Server, each additional index will have a negative impact on an INSERT and may help or hurt SELECT, UPDATE, and DELETE performance. There is also a limit to the number of indexes you can have on an object (table or view). I expect that MySQL is handling indexes in a similar manner to SQL Server.
Knowing more what your question is though about indexes and SQL Server, we may be able to offer more help.