IMHO, messing with ROMs can be a PITA, but others will invariably pipe in and say the same about getting 30yr old carts to work.
Honestly, I've primarily been using my Ouya as intented, to play indie games. I did download all the emulators initially, but never really used them as I couldn't be arsed into loading ROMs on it due to the fugly process of connecting it to PC prior to the mass storage update. Another thing to point out, sadly, is that Ouya's mass storage driver update last fall broke compatability with the Retrode. Before, emulators had to supply their own mass storage drivers to work with USB, but when Ouya updated their OS to support mass storage, they included support for NTFS and FAT32 but supidly forgot to add FAT16. The Retrode uses FAT so when plugged in, Ouya throws an error saying "Unsupported Device" and disables it. Now even the joypad ports on Retrode cannot be used anymore. I recently aquired a Retrode + N64 plugin and was a little bummed out it doesn't work on Ouya anymore like it did in the YT videos. All those vids on Youtube showing Ouya happily running with a Retrode, game cart, and joypad plugged in? Those were posted in June of 2013 BEFORE the fall mass storage driver update. Retrode compatability issues aside, Ouya is an excellent emulation console, and the USB storage update makes it eaier than ever to load ROMs on it. That said, as someone who has a nice assortment of retro consoles, I prefer playing the original carts. So I use the Ouya for playing indie games and original hardware for retro games.
My consoles aren't getting any younger, so I'm really looking forward to using the Retron5 to reduce the amount of clutter and reduce wear and tear on my original systems. With Retron5, I don't have to unpack my Famicom, NES, SNES Genesis, whatever and put it up afterwords every time I want to play a cart from another system. As for homebrew/repro/whatever compatability, I still have old faithful when I need it. Retron5 will complement, not replace my old game consoles. Also there are options like controller remapping, save backup (back up your savegame to the Retron5 before replcing the battery), built in cheats system where you don't have to use Google to look up the codes for your favorite game, save states, screenshot capture (though I'm still a little peeved they used lossy Jpeg instead of PNG), crisp HD display with loads of options, etc...
While both Retron5 and Ouya are $99 game consoles for budget minded consumers, the simularities end there. Retron5 supports carts only and cannot load ROMs (unless someone later hacks the firmware, which I believe has a good possibility of occuring down the road), and Ouya cannot load cartridges, however it does allow people to download ROMs as well as modern games. The two consoles are mutually exclusive in what they are capable of and I think it's safe to say that if you are trying to decide to choose one console, you will miss out on most of what the other has to offer.