What does it mean to "accept my shortcomings"?
I suppose the word "accept" you hear comes from the acceptance and commitment therapy, or ACT. According to the link, the healthy attitudes towards the problem (e.g. obesity) are:


Accept your reactions and be present
Choose a valued direction
Take action


So to answer your question, it is about accepting your reactions, your emotions about the problem, not the problem itself. An obese person can be shame, guilt or embarrass about their obseity, and they want to avoid such emotions. This, according to my understanding about the approach, means that they want to avoid facing the truth that they are obese, and thus the action to change cannot be followed. By accepting such emotions, they can dissipate them.

Therefore, it's not about you want to change nothing, nor finding the problematic situation satisfactory, nor believing you don't have such problem, but about accepting the negative emotions when facing the reality.