Bonuses for wearing all items in a set.
Like, you'd receive an extra bonus for wearing all of the items in a series.
It wouldn't just be mashing the numbers of the two armor items together, it would have a bonus that neither pieces can achieve alone. (unless you have like a unique variant of that kind on one item.)
Like say... for example, Wolver Cap and Coat together increase your attack speed of sword, or Salamander set has less weakness to ice when together.

At the moment, due to the very restrictive armor system, there's actually a huge penalty for wearing sets: each type of armor only protects vs 2 of the 4 types of damage.
If you don't mix and match with different armor types, you'll be dead in seconds come tier 3, which is really kind of unfortunate. (And even if you do mix and match, odds are that you'll still have no defense at all against one of the common types)
Though that may be the case, most people still choose to wear an entire set rather than just one piece from two sets as their actual armor, because of some bonuses.
Like me. I had the full Skolver set on. It gives me a Sword Damage Bonus: Very High, and it made my swords' damage boosts (vs fiends and vs undead, Divine Avenger and Cold Iron Carver) maximum.
It also made my Divine Avenger's damage shoot all the way to maximum normal and elemental damage.
:D
Though at the cost of any defense BUT normal.
Haha, nope nope nope nope. Noooopenopenope.
Very few enemies deal piercing, shadow, and... Uh... I don't think I've even seen an enemy that does elemental damage... Anyway. Normal is always a must, because it's the most common damage type. Anything else is just gravy to add on, and if you spread out your armor to get all four defenses, you're gonna die a lot more for having much less Normal defense than anything.
And not dying in tier 3 is based more on your ability... and if you didn't get stuck in Dark City. (And also having enough Normal defense to not die in one hit.)
I have seen lots of elemental damage. All gun puppies do elemental and most enemies on fire or frost floors will be modified to do elemental damage. I've also been hit by a lumber on an undead floor that did all shadow damage to me. While it is a very good idea to make sure all of your equipment has normal defense on it, it is also wise to get shadow and elemental resistance. The only piercing damage I have ever received was from spikes in the floor and the spike attack of a fully formed lichen.
Edit: Also to Magnus. I was just watching your Vanaduke fight and for the entire fight you where taking elemental damage.
The merged lichens (non-jelly oozes) deal piercing damage with their spike fling and thorny root attacks. They're just about the only mobs with piercing damage. Of course I found this out after making my Wyvern shield (whoops!).
Elemental is common. The beams on the mech constructs, flame thrower gremlins, all gun puppy attacks, and even some bat/kat/fiend attacks have elemental attached. Made me appreciate my Wyvern shield a good deal, actually. And of course, anything undead or fiendish will probably do sizable shadow damage.
If you're going tanky, mixing and matching can work I guess, but it makes you a jack of all trades / master of none.
I honestly believe it's more important to get a more appropriate armor set and picking a contrasting shield. I.E. if your armor has great normal and shadow but weak elemental resist, get a shield with great elemental so you can intelligently shield the most dangerous attacks.
Anyway, back on topic, set bonuses would be cool.
Oh, well. That explains why I never see elemental damage. I don't walk into firey floors on purpose, and gun puppies are easy to dodge.
And, for Vanaduke, I don't pay attention to what damage I'm taking. Any attention not payed to dodging and when to Remedy and glowing floors is a chance to get destroyed.

Personally the only set I owned was the Fallen Set (Only to have fun if I wanted to do crazy damage due to my unique variants + trinkets), but if you put two armor sets together you already are getting a bonus in a sense example: Crown of fallen has Damage bonus Low, and if you have armor of the fallen it has damage bonus low as well, but together they give you Damage Bonus Medium (which makes sense, and to me you wear armor sets for certain stat bonuses.) I choose to wear Dragon Scale Armor and Divine Helm (Forgot the real name), to get Fiend and Beast Bonus, and if I wish to get ultimate fiend bonus on all of my swords I would just equip a Divine Set.
The example you said:
Salamander set has less weakness to ice when together - Does this make any sense to you? If I wear two armors which both have a negative against Ice (even though they are the same armor set) I should decrease the damage I take against Ice....
Your Idea to have well a "special bonus":
I think honestly would make the game a bit too easy. Why you ask? If your a player like me who likes certain Unique Variants I would attempt to get lets say Shock and Ice Resistance high (1 for each), and knowing that having the set together I gain Stun Resistance I can easily have an armor which gives me great elemental bonuses on top of that great attack bonuses. Looking how the dev's, broke up the whole armor/helm system and made them well more mix-and-match I think this would make that action pretty much useless.

I've made threads about this in the past:
This one is all about sets and bonuses.
And this one is all about how they could look on armor.
I think this would be fun, I don't see it having a detrimental affect on the game. I have thought about this before too (similar to WoW).
I don't think the bonuses have to be anything too crazy, but I think if you wear all the pieces of a 2 or 3 piece set you should get some kind of bonus. And these bonuses could change / improve as you go from 2 Star to 5 Star versions of these sets.