Judging from what we now know its become apparent to me that weapon skills/perks no longer exist, multiple forums have gone around saying guns is now known as gun nut, but lets look at what gun nut did in fallout 3 +5 guns +5 repair, now lets look at where it was shown at e3, the crafting system right? Yes, so putting these two together leads me to the conclusion that gun nut is a crafting perk as is science since neither (realistically) would affect a weapons damage, lets be realistic here being good at science isn't going to make a raider's laser rifle hit harder, just like knowing the difference between a clip and a mag on a gun isn't gonna make it pop a muties head any better, it will however give you a better understanding of their inner workings allowing you to make modifications.
Need more proof? Well since its almost confirmed that weapons and armor no longer degrade that means that there is no use for a repair skill/perk, but Bethesda seemed to be focusing on crafting in their demos, so they must of split repair into science and gun nut and possibly a melee version (more on that later), made hacking its own thing and with combat being focused on player skill rather than "number crunching" its only logical to scrap weapons skills/perks all together.
So next melee and unarmed or should I say just melee since it seems they've combined the two, so
Lets look at the special stat descriptions shall we strength clearly says it affects melee damage whereas endurance doesn't mention unarmed, (since when does your endurance affect how hard your punches are?)it says nothing about energy weapons/science and agility makes no mention of guns/gun nut either, so we now know that combat is focusing on player skill + weapon stats, it seems strength will directly affect your damage output with both these weapon types.
Now lets look at perception, it mentions accuracy in vats directly, not accuracy with weapons nope accuracy in vats, so this strengthens my relying on player skill point even more, it also means that combat inside and out of vats will work differently, now before you go red in the face and grind your teeth to dust and scream "CALL OF DUTY WASTELAND WARFARE" let me give you a little good news regarding combat and "tactics".
Armor yes armor its layered now, that means that a raider's right arm could be more exposed than its head making it a weakness, meaning that you would aim for the arm to do the most damage and use the least amount of bullets, think of it like an old school boss battle in most rpgs you can just wail on the enemy till it drops dead or you can exploit its weakness, lets look at what Todd Howard said "vats now offers you more control" control to do what exactly? More damage as we can directly attack specific parts of our enemy exploiting their weakness, it may seem a little OP which is probably why it only slows down time instead of freezing it adding a bit of difficulty, so if you want fallout to be more of a tactical rpg than an fps simple just use vats an deal more damage while using less ammo by targeting your enemies weakness.
Although I have more bits and pieces iv already said alot so ill just check list these other points with quick descriptions, apologies for any misspellings or grammar errors in my writing im writing this out on my phone at work in short bursts so my boss doesn't see me.
-Power armor can be blown off to open weak points.
-ghouls arms can be blown off so that weakness is gone after a certain amount of damage.
-can command companions to take positions and attack specific enemies on the go.
-attack dog perk lets you command your dog to pin an enemy to the ground and rip its throat out as shown in the e3 demo.
-weapons show you all of their stats not just damage.
-heavy focus on special stats.
I'll try an add more info if I think of any and if anyone has any more information supporting or disproving any points I have made I would like to hear them and your opinions.
Since I explained this terribly I guess I should clarify, I'm not saying player stats are gone just that there will be no direct weapon skill like guns, but there will probably still be some like cowboy and grunt in the game.