In my experience Mendelssohn’s reputation has gone up and down with the reputation of Victoriana (Landseer’s paintings make a good parallel). Sometimes they are dismissed as outdated and vacuous, sometimes revived as misunderstood and containing unappreciated qualities.
I think contemporary taste colours our judgement of art more than we think. Maybe in fifty or a hundred years’ time a different taste will prevail and our age’s admiration for Messiaen and Stravinsky will be dismissed as naive and mistaken by a later age who consider them overrated.
I do find Mendelssohn very uneven, and this is emphasised when one hears so many of his lesser-known works. At his best he’s Schumann’s equal, if not that of Berlioz, but that doesn’t happen often.
It’s often said that what prevented him being a great composer was that his life was too easy; he never suffered the traumatic experiences which forged Mozart and Beethoven as adults. But I wonder how many people who think he’s overrated know the F minor string quartet.