Villi in the small intestine
Height:5'1.5 RNY:11/30/11 HW:307 SW:234 CW:136 GW:140 (LOST 73 Lbs. PRE-OP)

Actually, you're mistaken. The RNY bypasses very little of the small intestine, so even in the very beginning you're only malabsorbing a small per centage of the calories you take in. I don't have any numbers for the per centages of protein and carbs for RNYers, but there was a study that measured the absorption of fat. 'Normal' people absorbed 92%, RNYers absorbed 62%, and DSers absorbed a whopping 19% of dietary fat.
DSers, who in comparison to RNYers have a HUGE amount of small intestine bypassed, generally absorb about 50% of proteins, about 60% of complex carbs, and everybody absorbs nearly 100% of simple carbs, alas. (*grin*)
It's my understanding that they start regrowing right away, and around 18 months is when malabsoprtion of calories mostly stops. You can't really stop this, it's just a natural part of the body adapting.
Follow my vegan transition at www.bariatricvegan.com
HW:288 CW:146.4 GW: 140 RNY: 12/22/11
Your body sees WLS as a traumatic injury, and does its best to 'heal' from it. One way it does this is to grow more villi, to replace the ones that were in the part of your intestine that was bypassed. (Sometimes, your un-bypassed intestine actually grows longer, too!) There's nothing you can do to stop this, and everyone's body has its own rate of effectiveness at 'healing' from WLS.
But keep in mind that this does NOT mean you're going to be able to slack off on your vitamins and supplements. Micronutrients---in other words, vitamins and minerals---are only absorbed by specific receptors. You will ALWAYS need to supplement.
