Rotom and Volcarona must be the greatest cases of: "Wait, you're telling me they're NOT Legendaries?". Both were set up far differently from other standard Pokemon introduced in their Generation and within their debut games. In fairness, "interactable Pokemon" have always been a concept seen throughout the mainline series, though they were often utilized as roadblocks or small surprises for exploring. Rotom in DP, and Volcarona in BW, essentially had players beating the game as a requirement before they were given the opportunity to meet either. Furthermore, they were battled in some rather fancy locations. Heck, Rotom had the Legendary Theme for its unique encounter in DP. Every detail I recall or look into only deepens the mystery of these Pokemon further. Their Regional Dex numbers in their first games, and their National Dex numbers, place the duo of oddities just before the Legendaries introduced in Gen IV and Gen V. In Volcarona's case, it and Larvesta are placed AFTER Hydreigon and before Cobalion, which is very interesting. Another odd detail are their base stat totals. Rotom's possession forms have a BST of 520, putting it on par with a few third-stage Pokemon (Flygon, Klinklang, Aegislash, etc), and two full second-stages (Starmie, Exeggutor). Volcarona's 550 BST would later be tied with Urshifu, who IS considered a Sub-Legendary, and Ursaluna. Call me oblivious, or perhaps even crazy for reading into all these standard details, but Rotom and Volcarona seem as if they were meant to be some form of "Legendary", before being retconned into standard, albeit rare, Pokemon. Sub-Legendaries/Minor Legendaries, perhaps. Larvesta & Volcarona could have combined concepts seen with Manaphy, Cosmog's Line, and/or Kubfu & Urshifu. Meanwhile, Rotom may have been comparable to Type: Null & Silvally? Who knows, but it sure is fascinating!
Spiritomb is another one, though to a lesser degree. Wish Rotom and Volcarona would receive updated lore about this.