Before I begin, let me clear the misconception that the 3-year MTech program is inferior in quality to the 2-year MTech program. Because of this false assumption, the higher ranking MTech students tend to choose the 2-year MTech programs instead of the 3-year program.
Similarity
Differences
Both IIT Hyderabad and IIT Bombay offer 3-year MTech programs. There may be some other IITs as well offering similar programs.
Between BITS and IIT Hyderabad, I think the latter is a better option from a research point of view. Additionally, IIT Hyderabad also has a locational advantage, better connectivity, industry, expert interactions, etc.