Honestly, don't worry too much about this. Everyone has weaknesses.
Typically what's more important is that you are aware and working on
improving on your weaknesses, rather than trying to say that you only have
weaknesses that aren't really (eg. too much of a perfectionist, too
results-driven, etc). If your recommender asks for your input, you might
explore telling him what you think are your own weaknesses and what you're
doing to improve them, and then suggest that he make his own judgment on
what to write. (Sometimes it may also be unrealistic for someone to be
working on all his weaknesses at once too, so be wary of that.) | 
