I'm a bit confused.

Suppose: I roll 3 damage and 1 surge against my opponent, he rolls 1 defense.

My skill says: pay 1 surge: either +1 damage or gain 1 pierce.

Pierce means: negate 1 defense

so....

if I up my damage I do 4 damage -1 defense; totals 3

If I pierce I keep 3 damage and ignore his defense through pierce I get: total 3

Seems to me this choice is between an apple and an apple, where is the difference?

I made up a houserule for this that changes Pierce into : reroll 1 yellow die. This means, I could get also - 1 damage- but also a chance on 2 or if it fails a 0. Guess his armor was tougher..

Am I missing something in the rules?

In your example there is no difference which surge ability you choose. The result is the same.

HOWEVER

The ability is more useful when you roll two or more surges. The reason being you can use each surge ability only once per attack. (RRG p. 24) If your weapon has +1 dmg and pierce 1 as surge abilitites, you cannot use more than one surge on each ability per attack.

Pierce is slightly weaker than raw dmg increase, but not useless by any means.

You are free to create houserules, but your current one is VERY powerful and can lead to weird conflicts where you roll surges but do not have any yellow dice in attack.

Point is I like my skills to have that 'special' effect than just add 1 dam. - ' Yay pierce' ! +2 dam ! (1/6 chance) or fail (2/6 chance) Do I go for the pierce or just give 1 dam.?

But, you pointed out the rule I overlooked, surges can only be used once, so thanks ! I'll reconsider.

Early in the campaign it is just the choice between "an apple and an apple" but as the heroes gain more XP and abilities and better equipment the difference becomes more relevant as Krankenstein pointed out.

Pierce 2 or Pierce 3 gets to be really relevant later on.

Against a highly armoured opponent like Vader or an AT-ST, Pierce could be a fight-winning ability. As long as you roll more tahn your pierce in damage, you'll always inflcit your Pierce in damage (unless the opponent's defence roll is double your damage roll, or your up against the dreaded evade face of the white die!)

I strongly recommend against house-ruling pierce. As others have stated, it may seem lackluster in the beginning, but it is supposed to be that way. Overall power in the campaign setting ramps up as the missions progress, and you will quickly find your house rule to be insanely unbalancing.

In your above example, you did find a situation where Pierce 1 and +1 Damage end up granting the same net result, but you will find situations where making the choice between Pierce 1 and +1 Damage matters.

Had you rolled 3 damage and 1 surge, and they rolled no defense (or had their single defense die removed). Pierce in that situation would be wasted and you instead choose the damage.

The choice between damage and Pierce gives you flexibility to deal with the rolled outcomes.