The only answer to that is 6.1 does a lot more, faster, and has a totally differnt look and feel.
There are huge differences between 3.5 and 6.1. You'll need to read all the release notes ( especially for 3.6, 4.0, 4.3, 5.0 and 6.0) to work out what differences are a concern for you.
"Reporting feature" is too vague a phrase to even begin to guess what functionality you might be asking about.
I'd suggest instead of asking wide ranging questions with no answer better than "read it for yourself", you tell us your worries. 6.1 and 3.5 are both still fundamentally issue trackers, trapping issues with updates, fields, workflows, and user activity. But beyond that, the decent answer is a several thousand word essay, and none of us here are going to write that, only to have you ask even more questions on the bits that actually matter to you.
If you mean a "Custom Reporting" feature, for making your own reports, there are plugins available as well as you can make reports with some REST/SOAP programming. I use 5.2 right now and we're upgrading to 6.1 and there is no native Custom Reporting feature in either one but we have loads of options and loads of built-in reports.
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