It simply cannot be stressed enough that you should, without a speck of doubt go for IIIT Vadodara. The reason I recommend this institute with so much confidence is that my friends are alumni of this same institution. Therefore, it is suggested that IIIT Vadodara will prove to be better for you than IIIT Kota for pursuing CS. 

If you make a comparison between IIIT Vadodara and IIIT Kota, I would consider every aspect that essentially includes vital factors like the faculty, study/work-environment, etc., and having experienced the best of all of that's mentioned. 

All in all, it is recommended that you definitely go for IIIT Vadodara. The faculty here is pretty good and DAIICT is the mentor institute. You simply cannot say NO to a place that comes with such a fine faculty. Other than that, the choice is yours as only you will know what's best for you.