I don’t think you should even consider joining IIT Hyderabad EE when you have the option of IIIT Hyderabad CSE given the fact that it’s the 2nd best in India after IIT Bombay CSE. The course is very challenging and IIIT Hyderabad does not have a lively atmosphere like IITs. Rather, the entire focus is on CS courses and research work. Although the campus is very small and lacks any extracurricular facilities, it’s heaven for coders. The academic workload is terrible with intense competition among peers.
Overall, both are excellent choices, and it’s only a matter of preference. Go for IIIT if you are certain of CS and go for IIT if you aren’t sure of your inclinations. Either way, you will not be disappointed.