Spoilers for season 2 finale
If you haven't seen Agents Of S.H.I.E.L.D season 2 Finale, You Have Been warned this contains Spoilers.
At the end of the Agent Of S.H.I.E.LD season 2 Finale we see Terrigen Crystals in the ocean being absorbed by fish that then get turn into food/health products, which is there way to introduce many Inhumans that cannot control there powers to keep things interesting in the Marvel Cinematic Universe, especially for Civil War as in gives some understanding on why the government want to register Super powered people even though we are only seeing the main heroes in Civil War.
This creates an interesting dynamic for Marvel To use as now they don't have to explain how most characters they got there powers, its just simply there Inhumans.
And now with season 2 over I have came up with a list of potential villain we could see in season 3 with minor over a couple of episodes and major villains that could possibly effect the entire Universe.
After his appearance in the start of season 2 I was hope to see more of the Absorbing man Unfortunately it didn't happen, but there is potential for this character to evolve and maybe be able to make his hands into weapons.
The Wrecking Crew (Thunderball, Bulldozer, Wrecker & Piledriver)
The Wrecking Crew are interesting Villains cause they more well known Marvel Villains but obscure enough to be used for [Agents of S.H.I.E.L.D.](tag:722469), They all have Super human size and strength (in comics due to Gamma radiation I believe) which they could do or they could go down the Inhuman route.
The Tinkerer is a small Spider man villain who mostly gives other super-villains there technology which would be a easy way to hint or even introduce Spiderman through Agents of S.H.I.E.L.D.
Hydra - Viper
Even though Hydra was a big deal in Season 1 and the start of season 2 they have been hurt real bad after many of there heads we already know that Baron Zemo is one but probably isn't going to appear on TV and another could be Viper, also known as madame hydra he is a known assassin and almost a mirror of Black Widow and I think that she and hydra will show up not as much but just enough to know they are there.
We already know that he is going to be a Villain in season 3 cause in season 2 he was and wasn't a villain he was really for himself but after the finale we know that he is pissed and wanting to kick ass.
A Villain that was set up from about 7 years ago is the leader, know with no Hulk movie in development the leader would work in agents of S.H.I.E.L.D as he is a gamma radiation villain who is been given super intellect and has had 7 years to come up with a plan to conquer that be S.H.I.E.L.D, the United States government or the unite planet only the leader knows.
Taskmaster is one of the most deadly assassins in the marvel universe and would be an true treat to the team, normally he recruits/trains supervillains and henchmen but is known to be a very dangerous villain to face.
There has been some talk around the internet that Ward could be taskmaster, but I don't think he is mainly cause task master technically has a superpower, which is that after seeing someone do a move/fight style he can do it and I don't believe that they would make another character Inhuman cause it would be too much coincidence that Ward is inhuman as well as daisy/skye and possibly Simmons.
A.I.M - M.O.D.O.K
A.I.M was introduced in Iron man 3 and after that pretty much disappeared, I believe that now hydra is less of a threat and is regrouping, reintroducing M.O.D.O.K and A.I.M as another obstacle for S.H.I.E.LD and the Marvel Universe, but they would maybe have to tone M.O.D.O.K down cause he looks pretty stupid.
I feel Wonder Man is such a interesting powerful character but when I talk about him to friends there like he has a Stupid name (like most characters) and isn't known that well to make it into the avengers, but Agents of S.H.I.E.L.D isn't that bad of a place for him it gives them more time to develop his character, because in A comic story Wonder Man starts off as a owner of a slowly failing engineering company after Tony Stark buys his company behind his back, he under goes an experiment to give him the power to get his company back (energy lasers/blasts, flight, super strength etc) after releasing some anger he realises that what he was done was wrong but is forced to fight against the avenger when he found out that his new powers will kill unless he works for Baron Zemo who has a temporary cure for his illness, but after sometime becomes a superhero.