There's a problem with jumping too high - you'll hit this invisible ledge on the way back down. I found a fix for it though. If you walk off of something high up, you'll fall smoothly to the ground, but if you jump equally high, you hit the hangup. So I've got some code in my Powered Power Armor mod that spawns an object under your feet at the top of your jump. You land for a frame or two, then it deletes it and you fall to the ground like you just walked off of a ledge - uninterrupted.
The timing would be tricky, but I think if you did something similar - spawned something under the player's feet - they'd be able to jump off of it. Maybe continuously spawn and delete objects as long as the player is on the way up (zPosCurrent - zPosLast > 0).
I was thinking of splitting that code out of my mod into a separate module - a number of mods could benefit from it, but it only needs to be included once in a load order, not with every mod that needs it.