With regards to Rei, her being a clone I think is the most likely answer. Remember she needed medication to stop her from literally rotting alive. I would imagine she suffered from stunted growth.
With Shinji, he could just be a very late bloomer. He might grow a lot as he ages and be as tall as his dad.
With Asuka, she is slightly taller than Shinji, but still quite short. Although the drawing varies wildly due to budget/lazy animators/teh lulz, she never seems to be hugely well developed (her breasts are still fairly small) so once again she could be a late bloomer.
Applying real-world logic to the whole cast, Japanese people are quite short compared to Westerners. Case in point (as I've said before in fact), my friend/crush Hiroko (who is from Kyoto) is actually older than me, and is approximately an absolutely tiny 130 cm
(this is just me judging by eye, as for obvious reasons I haven't actually measured her). For the record, I'm not especially tall, but I'd have to kneel down to kiss her (if I ever got that close with her...
). Likewise, my Japanese teacher Kumi (who fairly obviously is much older than me) isn't quite
so small, but is still pretty short.
Here lies Squigsquasher.