Hey Yash ,
Greetings!

Both institutes are good for JEE aspirants but there are some points and features to consider,

RESONANCE

• Good teachers, only if you manage to be in good batches, otherwise neither the teachers nor the Institute care about the lower batches.
• Study material is good, only if you attempt it regularly. More than enough material is given, which sometimes creates a mismanagement in order to attempt it all.
• Quantity wise you'll find thousands of competitors, but only few hundreds are good enough to stand in the jee competition.
• Test paper levels vary a lot, though the patterns are very good, which will make you ready for any type of pattern. Test frequency is acceptable.
• Frequency of classes is very comfortable in the two year programs as compared to the other institutes.

FIITJEE

• Its best study centre is in Delhi, which isn't a very good choice as compared to Kota.
• Test paper levels and frequency is the best as compared to the others. Tests are slightly tougher than the real JEE.
• FIITJEE is known for its top ranks and % selection ratio. Resonance has a very low percent of success ratio.
• You'll find many intelligent students around you, while in resonance the number of dumd students is higher than the intelligent ones.
• Its study material is not meant for boards or mains, but very much good for JEE advanced.
• Their review packages are good enough to save your precious time when jee is near.

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This is the best that I know about these two institues, but I would say that if you're smart enough then it doesn't matter a lot.

After all, it depends only on you how you study and what kind of environment suits you.

Hope this will help . Good Luck ! You can reply to this comment if you have any further queries , I will be happy to help .