It's a weird place to discuss Mendelssohn's merits (would be more suited to the "overrated" topic), but ok.
I think it's a problem of personality. Since M. was an early 19th century composer, we tend to regard him, historically, as a romanticist - which he was to a certain extend, but far less typically than some of his contemporaries like Schumann or Chopin - or even predecessors like Beethoven and Schubert. Thus, if we're expecting M.'s music to be full of the "romantic spirit", we're gonna be disappointed.
Romantism assumes conflict - between form and content of a composition (like Beethoven's) or even between the different personalities of the composer himself (Schumann!)
Nothing of that with Mendelssohn - he was a mentally stable guy who lived a relatively carefree (yet way too short) life and his music reflects his easygoing personality. No towering highs and lows, just the slightly apersonal distinction that makes him look more like an elegant 18th century gentleman than a troubled romanticist. Whenever there's some "Sturm und Drang" found in his music, it's handled with a tongue-in-cheek approach.
That said, I don't agree with people who dismiss his music as "superficial". Because that would mean assuming that all "depth" in music stems from contrast, conflicts and heavy emotionality. A rather unemotional piece with a perfect balance between form and function can be as "deep" as a heartfelt masterpiece that leaves no emotional key untouched. See Bach's often called "cold and mathematical" late works. Apollo resides at the Olympus too, not just Dionysius.
But it's true that while most of Mendelssohn's music is good, brilliant even, it isn't often "genial". And after the amazing abundance of masterpieces written in his early years, there's hardly a progression in style: there's just more of the same. If he had the same progression from a child prodigy to a mature composer like Mozart, he'd be the greatest composer of the 19th century. But instead, many of his later compositions fall flat, and appear to be the products of a conservative mind, who was content with his style and lacked any impetus to develop or improve it. Some musicologist whose name I forgot once said that Mendelssohn was already an old man when he died. One can assume that if he had a stronger heart and was lucky enough to live to an old age, he'd become the biggest conservative old fart of all Germany. Or maybe not, who knows.
Schumann has this problem too - brilliancy in his youth, mediocrity later of his career. But in his case it was the result of a restless mind that urged him to explore new genres and new styles beyond the area where his true strength lied: piano and small-scale vocal works. In Mendelssohn's case it was more of a case of a mind that wasn't restless enough.