Until now, anyone with an 11.2 3DS would either need to get a hard mod or find an already-hacked 3DS in order to reliably manage save files for use with PKHeX or play ROM hacks. These requirements are no longer applicable thanks to the 33c3 conference revealing several 3DS exploits today. Here are some highlights of its findings as it relates to the 3DS:
Soundhax - Excellent, convenient, and free userland primary that hacks the built in sound application with just an MP3 on the sd card. Will be released soon according to nedwill.
Fasthax - New arm11 kernel expoit (like memchunkhax, waithax, etc.) also by nedwill. Works on latest firm and should be released soon just like Soundhax. Should allow nfirm downgrading on latest firm when more advanced dsiware injection techniques are released very soon.
Method to dump arm9 bootrom detailed by derrek. Hash given as proof. The same technique has been worked on for months already by #Cakey devs, so this will likely take quite a bit more time for a public dump to show up. One benefit of bootrom dumping is faster PC based crypto stuff instead of slow 3ds methods. The second benefit is the next exploit:
Sighax - The big one. Flaw discovered in the bootrom's RSA parsing process of the 3ds's firmware partition. This will allow us to sign our own custom firm and no more having to do risky downgrades and 100 step guides to get the OTP. Unfortunately, we need a bootrom dump to implement this and that is an issue, see above bullet point for why. You will also still need a way to actually write to system NAND, and even k11 hax usually isn't enough for that. Hardmod is also an option, but it's expensive and inconvenient. That should always be an option, at least, given sighax itself is unpatchable without hardware revision.
If you read either of our save management guides (NDS or 3DS) and needed to purchase additional hardware, you are advised to wait until these exploits are released before actually buying anything. While your purchase would likely still do what you want it to do, free alternatives are coming soon.