Well, over the 3x00, the 5500 has:
- a larger, articulated screen (this can be a big thing)
- builtin wireless
- touch screen
- more focus points
- TIMELAPSE RECORDING
- AEB
- bluetooth
Yeah, you can buy an add-on for the 3x00 to do interval shooting but the 5500 has it onboard. That's handy. For stop motion work, that alone would make shooting go a LOT faster.
Per dollar, even tho a refurb, I do think the 5x00 series is a better choice (I don't think the prices are that much different to justify the cheaper camera). The bracketing and wireless are really convenient too. And the ability to move the screen around, for stop motion, would be a big plus.