As to what is 'best' you do need to factor in things like how much you like the bike, your mechanical skills and how much you enjoy working on bikes.
From a financial perspective, look at it his way:
Non working 2001 two stroke 125: Worth maybe $300, not easy to sell
Parted out 2001 two stroke 125: Maybe you'll get $600, if you spend lots of time on ebay, craig's list and arguing with a 15 year old about whether your rear brake disc is worth $20 or $10. Stuff like forks and the pipe are marketable, but a pain to pack and ship.
Fixed Up 2001 two stroke 125: Maybe it's worth $1300 running, but you will have to spend the $800 in parts, buy a shop manual, fix it yourself, etc... But at least you can do the work on your own time.