I always give the same answers to these things, but what the heck:
Mac Gargan/The Scorpion: Four years ago (almost), I basically wrote a long (over 100 pages in WORD) fan-fiction depicting my revamped version of him and how much of a threat he could be to Spider-Man. He's spent too long as a raving mad lunatic who relies only on strength and a mechanical tail. He needs the cunning mind of a detective to match that. Combine the two and he could have been a rival to match the appeal of Venom.
Hydro-Man: My approach, which I did in my very first fan-fic (which I only have in printed form now) was to make him a sort of eco-terrorist, someone who wanted to "merge" with the entire ocean and make the world pay for polluting it. While this made him more dangerous and his imagination over his powers grew, he was still a thug who wouldn't care about the havoc he did to both land and seas to attain his goals. While he pretends to care about saving the ocean, he really just wants power and recognition. Given a boost, he could easily occupy a team of heroes.
Mandarin's Son: the Mandarin himself is dead, so the key to enhancing his legacy is doing something with his son. Why not take a cue with the LOTR? Maybe Mandarin's soul is inside the alien rings that his son now holds, and maybe he seems to want to help steer the boy in "his" direction. Not quite posession, but mentally influencing his son to do what he wants, like any father would. His rings allow him to be powerful enough to take on a team of heroes if applied properly. Mandarin always wanted conquest, but why do it like an idiot when you have a hypno-ring? The son takes the slow burn, which is harder to undo over time. Just influence the right people, make enough appearences, make the heroes unsure of who's the servant and who's the master.
Graviton: someone who's got a Magneto-level power and nothing to do with it.
Count Nefaria: As people said, he's essentially "Superman as a Mafia Grandfather". I've heard of many mobsters who bemoan, "if only I had my hands on him, I'd strangle him" or something. Nefaria can be boss and enforcer in one. And he's tough enough to fend off even the best line-up of Avengers. He escaped prison in the first issue of NA, now he needs to knock Kingpin off a peg. Here's a clue; TAKE OVER THOSE AREAS BETWEEN NEW YORK AND CALIFORNIA. Make a whole supervillian mafia where they literally divide states and major cities in those areas. By the time heroes sniff what's up, the roots in it are already hard to stop.
Shocker: I could see him leading a plucky band of the Masters of Evil. They're not after fighting the Avengers, just watching each other's backs to commit robberies here and there, sort of like Capt. Cold and the Rogues. Shocker's smart enough to cobble together weapons from prison-scrap; I sort of see him as being akin to Techno (from Thunderbolts), only maybe a few pegs down (which is still impressive). Shocker has a gimmick for sound/air currents, that's fine, he can keep that. A shrewd enemy who's after money instead of glory and knows when to cut his losses can be formidable. Just ask Taskmaster.
