Frist of all bring back pass/fail if fail you get the worst possible outcome for what you are trying to do or get the item in question destroyed. Also in Fallout enchanting is replaced via Science based stuff. Also you should be able to learn all the skills/preks brought up in this, using Skyrim as a base if its 3 or 4 paths to upgrade the first path is easy the next path is hard the third and fourth path is hardest. I really hate locking out paths but some difficulty mechanic is not so bad an idea..
Basically I would like to see a system where you can stack status’s and effects. Say you want better lather armor outside of remaking it as a higher quality set you should be able to apply some basic metal and leather bits to enhance its protection stats. So the main stats for armor is defense, magic defensive via natural material(or for Fallout effect protection via conventional non super science skills), weight, speed bonus/penalty and condition/degradation if applicable. You could break these up into categories to refine each of their bonuses.
You always have a chance however small to apply positive stats but most of the time you are going to get penalties with few bonuses, the higher level you are and the better your material is you have a better chance of applying positive stats. The ratio should be something like 1 in 200-500 for all positive stats starting out. You can also take stuff apart with a 90% fail rate starting out, to fail means you get a few basic items from whatever you took apart to successfully pass it means you get the best possible materials of tis construction from it.
Enchanting works in a similar fashion, albeit you can transfer an enchantment to a blank scroll this process has a high fail rate starting out leaving the piece of equipment highly damaged, the better the scroll and your skill level the better the possibility of error free transfer.
Spells work like skills in that you transfer a spell you gain a small amount of skill like points to that spell general type IE all fire go to fire the more you do it the higher your knowledge of that spell making it easier to apply and transfer.
No spell or blessing is immune to this transfer process however its broken up into 3 categories unknown with a 99% fail rate at very basic starting point level, blessing which are at a 75% and normal spells which are around 45%.
Stacking enchantments is rather easy if you succeed in applying a transfer you get a very small amount of that spell applied to whatever you are enchanting. The higher the spell level the higher the amount you learn of that spell type. Enchanting is broken down into 4 categories Affect(time in use, radius,constant effect,ect)Aquire(used to select specific targets of the spell like general types of undead, giant, dragon, light armor-FO, heavy armor-FO, anti personal-FO, anti armor-FO, ect) Protection variations and Offensive variations.
So if you have fire or healing, constant effect and radius you can make a flaming item that dose damage to anything near you.
Now for the fun bit whatever it takes apply and raise the stats/effects on equipment its 3 times harder to apply a NEW effect or stat, a fail in this will result in you turning your carefully tweaked armor into poo. LOL
edit
And now I recall something, instead of a hard fail where the thing is destroyed you do damage to its bonuses and raise its penalties , so you keep working away at it losing only consumable items that are reasonably replaced, the more rare it is the better your chance to raise positive stats.. For adding new stats it gets it gets twice as hard per new stat. That's a better system, maybe make a hard fail rare and kinda random based on your combined skills and equipment,ect.