For me, this drama is a bit of a mixed bag.

On the one hand, I find the writing for Lee Young Joon (the ML) and the complex relationship that he has with Kim Mi So (the FL) is very good.
Seeing how love changes people is always a treat for me, even though most of the times the characters that undergo this kind of transformation shift their personality 180 degrees, basically becoming a new character in the end. On the contrary, in What's Wrong with Secretary Kim, ML's character growth is done is such a way that he gets to keep his cocky personality throughout the whole story, but he gradually shifts from vanity, self-centeredness into a playful overconfidence that he gets to use in a very adorable way, childishly hoping to impress the FL with its boldness. Lee Young Joon is a many-sided character and despite the arrogance that he displays in various circumstances, he remains a very likeable character from the beginning till the end. Not for a second have I hated him or considered him despicable in any way.
The relationship between the main leads is also complex and multi-faceted. They have overall a very healthy connection and the topics chosen to showcase how one learns to overcome the difficulties of being in a relationship are right on point. Compromising, quick forgiveness to avoid extending conflicts indefinitely, putting your partner's need above yours, sacrificing your own desires, being considerate of your partner's feelings - these are all very well presented and even those that have a long experience in dating could learn a thing of two from this drama.

On the other hand, everything that did not involve the main leads was extremely nonsensical, annoying, unfunny and straight up boring. The various secondary office romances were just not interesting and felt much more of a filler than in any other drama I previously watched. Apart from one endearing character (Yang Cheol), I wanted to skip basically every scene involving these characters. The writing was so different from the one regarding ML+FL pairing that it always felt that one writer (a good one) was tasked to write the main leads story, and another writer (an unskilled one) had to handle everything else.

Lastly, even if "What's Wrong with Secretary Kim" is often compared to "Business Proposal" or "The Secret Life of My Secretary", I find these three dramas quite different from each other (despite them having common elements and even identical scenes). "What's Wrong with Secretary Kim" focuses on complex relationship development, while "Business Proposal" and "The Secret Life of My Secretary" gravitate around the idea of a double identity. They're all lightweight dramas, without any substantial plot and all three have a cold-hearted boss as ML with more or less a childhood trauma, but each of them has its own unique charm. "What's Wrong with Secretary Kim" probably has the deepest meaning, "Business Proposal" has the most likeable ML and "The Secret Life of My Secretary" the most memorable side-character (one can never forget the legendary "Veronica Park speaking").