Same problem and frustration here.
Enjoyed and am still playing FO3 so was eager for this. Played last night and at first it seemed good. The more I played, up to just getting out of the vault I realised I was getting more frustrated with the keyboard assignments, and found myself last night spending more time looking for a possible workaround than actually playing the game.
As with many others, for years and in many games, I use the arrow keys to move forward and backwards and to strafe, turning and looking up and down with the mouse (y inverted), R shift to sprint, R ctrl to crouch/sneak, Enter to activate, Numpad 0 to jump, numpad 1 or numpad del to reload and the end, home, page up, down keys for vats and inventory etc.
As with previous posters I found myself applying, and wasting, stimpaks at full heath, when intending to jump, and as also mentioned the looting was confusing, ie using enter (activate) to loot single items, while then having to look at the keyboard to hunt for the e key to loot from a container. Also looking for A to turn the locks while I could do it with the arrow keys in FO3.
So in the end, I was at work during the day, eagerly looking forward to getting home and playing, and as the evening went on my persistence to persevere with it finally wore off and as said, I found myself trawling the net for solutions, as I have done now this evening lol.
I would really still like to be able to play it, so I don't think i'll try for a refund (if I still can). I've just downloaded autohotkey so will try that.
Edit. For me I have put jump to my right mouse button as ive used on occasion before, and put aim to the middle button. The unlisted reserved keys seem to be for inventory items selected as favourites. I moved stimpaks to key 4 so that prevents me using them unexpectedly, though I think I only have one left, while numpad0 now does nothing if pressed out of habit for jumping. All though not ideal, I can live with having to look for and press the e and a keys as I would be stationary anyway when looting or picking locks. At least the game is now more playable and hopefully enjoyable.