Honestly it's not that awful, you can get to like 900kb~1mb/s (max) download speed through ftp, averaging around 600~700kbs. VC files can dl'ed fast, even for cias that're less than 1GB. If it's something larger than 2GB or more, it will take some time, add it to the time it'd take to install the cia with FBI.. You can skip both and just install those with custom-install on your pc instead imo.speaking of which, I only use ftp for small files. I have a n3ds xl too, so I have to use a screwdriver to take off the back plate every time for something larger than a few MBs.
Funny, for some reason i could never get SMB1/micro sd management to work with my laptop. Good thing ftpd works just as good..Sure, but it takes like 2 minutes to install it.

I do have access to the entire SD card using the SMB1.0 / in-built SD card management method. Here is the guide I followed:maybe, but that's the reason it's disabled by default. they're up to smb 3.0, I think. the ps3 and the 360 also use smb 1.0 to map them as a network drive, so it no longer works without it enabled. you can map them as a network folder though, so it will be like dev_hdd0/packages , dev_hdd0/PS3ISO , etc as separate drives connected, but I don't think the 3DS can even do that, and even if it could, it would be a mess not to have access to the whole sd card, just folders in it. it won't be the whole drive.