Much theories have been theorized over the 3 classes of devils fruits. I would like to discuss, and possibly be right about my own theories. Paramecia and Logia, for one, have people in great stupor over some seemingly conflicting properties. Zoan… is pretty clear cut though. I'll put forth some of my own definitions.
"Zoan" might come from "zoological", which means "Of or relating to animals or animal life". Zoan is also an ancient city of Egypt, in the eastern delta of the Nile. How this connects might be because supernatural beings might have been viewed mostly or all (?) in animal form in Egypt. A human getting the power of the devil and being able to change form to a beast would best be attributed to this ancient city? More plausible is Zoanthropy, a medical condition where in a person believes himself to be an animal. (thanks to Ubiq for pointing this out)
This devils fruit allows the user the ability to change his form into any animal. So far, we have seen mammals and birds. We can't say for sure that people can become reptiles, insects, molluscs and arachnids as of yet.
The user has 3 forms; human (normal), animal (corresponding power's) and the in between half-half form. With special radiations, new forms that mutate a particular body part may be borne from the regular 3.
A Zoan user has great ability to increase physical strength if their corresponding animal is physically strong. If in human form he increases at X, his animal form will correspondingly increase in strength. For example, if a bear is 5 times as strong as a human, a human training his muscles to X strength would equate a bear having 5X strength in the same amount of training. Hence, Zoan is the strongest in close range combat.
_Logia is a term applied to collections of sayings credited to Jesus and used as source materials by the Gospel writers in the writing of the familiar canonic narrative gospels. The Greek word "logia" means "oracles, divine responses, utterances, or sayings." The transformation to "elements" might indeed be seen as a divine response.
The Logia fruits give a user the power to transform to and fro from a matter/non-matter to flesh form. Logia users are invulnerable to physical attacks because when you are Logia, you become another thing altogether, and this other thing is particular/non-matter.
Logia users have the ability to manipulate their respective elements to a limited extent. Of course, nature has the ultimate power over them. This is seen when Crocodile's conjuring of a sandstorm became to ferocious for him to handle, although he did set it off in the direction of Yuba. This is also seen where Ener rains lightning bolts down accurately on the island, but only with the help of a souped-up thundercloud, which he must manually manipulate.
What I think is that a Logia will be invulnerable to any attack unless they are unable to switch into their respective element. For example, with water, sand becomes mud, but Crocodile isn't a mud-man, he's a sand-man. He has the power to turn into sand, not mud, hence if he was wet, his powers would cease to exist momentarily, because one cannot be wet sand; it simply does not exist (or if you want to be technical, sand is mud when wet, and does not retain its sandy properties).
As for Ener, it is the same reasoning. Ener is able to escape whatever is thrown at him simply because the assaulting objects are conductors of electricity, thus he is able to phase through them in electric form. However, when Luffy punches him, he tries to phase through Luffy but fails, because rubber is a non-conductor. Therefore he retains flesh form and gets hit. The same applies for all Logia users.
To sum up, I believe that Logia users are "weak" to a particular substance or circumstance because either their Logia bits only exist in the form of their Logia bits, with strictly no (or very, very little; enough for the power to overcome and disperse/ignore) variation (for matter Logias such as sand and smoke) or their Logia power simply cannot exist in another substance or circumstance (electricity and fire). Hence when these bits of themselves are confronted with their weakness, they have no choice but to subconsciously snap back to a human body.
Logias are only invulnerable to attacks and only when their Logia forms aren't presented with a counter. This is because attack or no, as long as it does not upset the Logia powers, no damage will be taken by them. A wet hand striking croc would do as much damage as a stream of water bashing him. The Logias will still retain their properties when getting hit by other attacks, so if an electric current is run through the conductor smoke, smoke bits of a user would not get damaged, but it would conduct possibly to people nearby or part of the DF user that was not in smoke form and do damage._
_Paramecium are freshwater ciliate protozoans of the genus Paramecium, usually oval and having an oral groove for feeding. Perhaps Paramecia was named so because the very cellular structure of the user has been altered permanently.
With a paramecia fruit, it is anything other than being able to transform to and fro from a matter or non-matter and being able to transform to and fro from an animal form. In paramecia, the sky's the limit. I believe I can classify paramecia into 4 main categories. Body alter, environment alter, substance emission and body change.
Firstly, it is the body alter category. Those that fall under this category include Gomu Gomu, Sube Sube, Supa Supa etc. In each of these, the body becomes rubbery, frictionless and metallic respectively. There is no command over the substance itself, only over the user's body. In my personal opinion, I would say this is the weakest devils fruit, though it can help the user out in a pinch. This is the only kind of fruit that gives the human body new properties aside from Logia, but in this form, the change is permanent.
Secondly, there is the environment alter category. The only one I can think of is the Doa Doa fruit. It allows the altering of an object's properties when in contact with a user. The Doa Doa fruit seems to be the first of it's kind to me… Their bodies also will still be in human form, it seems.
Thirdly, there is the substance emission category. Users create an object from their bodies, but their bodies are not that object. Their bodies remain in human form. These include Doru Doru, Hana Hana, Noro Noro and Ori Ori. They create wax, body parts, the Noro photon and cages (of an unknown substance) respectively. Unlike environment alter, they create new substances and do not alter ones present in the environment.
Finally, the body change category. The users of this category retain their human bodies but are able to rearrange their cells to form a higher density or just a new form for themselves. However, all the while, they still are flesh and blood. Examples are Toge Toge and Kilo Kilo. The first one creates spikes and the second one increases weight. They are still in human form when their powers are in activation. Unlike Supa Supa where the user is steel, these are still flesh and blood although in different shapes and densities._
Seastone and the Sea
_Seastone is a stone that emits invisible waves that weaken DF users. For Paramecia users, they become unable to do the respective of their class, ie emit substances, alter the environment or alter their bodies at will. Those that have been permanently changed remain changed, but as all others, their muscles also become extremely weak. Logias revert back to human form, but for Zoan, they suffer in the current form their body is in. Touching a seastone temporarily weakens DF users, but in minute quantities, their powers are merely arrested, and they have their normal strength still.
As for the sea, it appears that DF users are unaffected by splashes of water. It also appears that they will be unable to swim in water where seastone subtances are present. They must be almost totally immersed in a body of water for the same effect that seastone gives to take place. They become extremely weak but still have limited movement, but very far from enough for propulsion._