First: I totally agree that the repair skills should be gone. It makes no sense that someone who is a skilled blacksmith would be unable to repair weapons, or a skilled armor maker would be unable to repair worn armor. If you can make something from scratch, you can surely sharpen or repair it when it gets damaged.
Second: I don't know anything really about armor making (so feel free to ignore everything I say about it), but I do like the idea of some "gem" or "jeweler" skill which would cover gem cutting, jewelry crafting, and possibly the ability to appraise other peoples' jewelry and magic armor to determine their value and effect? I think the jeweler skill would cover fitting a gem into some kind of mount, and the armor making skill would cover the placement of this into an actual piece of armor. A jeweler skill would also open the door for custom jewelry, for character decoration and/or for enchanting.