For both the O3DS and N3DS, sysNAND must be on 9.2 or lower for the console to be exploitable. emuNAND for the O3DS can go up to the latest version; emuNAND on the N3DS can go up to 9.5.0-23. Some games will not work by default on the N3DS due to this limitation; however, cryptofixed versions of these games exist and those versions are playable on the the N3DS. They both have the same options when it comes to homebrew, I'm not sure if any homebrew has utilized the extra cores in the N3DS's processor. CFW is achievable on both the O3DS and N3DS without Gateway or Sky3ds.
There are a few N3DS exclusive games that the O3DS will never get. Not a lot of games utilize the better processor in the N3DS, but it does make a noticeable difference on the games where it does. I believe everything the C-Stick does can be done on the O3DS by using a Circle Pad Pro. The N3DS does have better 3D, but I never use 3D personally.
I like the N3DS better personally, but the the O3DS is definitely easier to use for CFW/homebrew purposes. You may have a tough time tracking down an exploitable N3DS now though. In the wild they are quite rare at this point. Instead of searching for one, you can buy one from a scalper online for an increased price, but at least you'll know it's guaranteed to be exploitable. There is a thread
here with a list of serial numbers and which firmware versions apply to those serials if you're interested in tracking one down.