Shouldn't Rei be younger than Shinji?

I don't know if this is a serious topic but its one that I can't figure out--shouldn't Rei be younger than Shinji? In the manga at least, we see that Shinji is about 3 or 4 when his mother "vanishes." We all know that Gendo uses Yui's DNA to create the Rei clone. That means she has to be at least 3 years younger than Shinji right?

I guess it could be explained that her growing up process could be different than others but this is never talked about. We clearly see that Rei "grows up" because we see that she once a small child. There is also no indication that she grows up faster than regular humans. For example no one comments--"Wow Rei, you suddenly got a lot taller!" and we suddenly see Rei is 5 inches taller than the other pilots. However, no comments on her blue hair either so maybe that is a moot point.

My guess is that they wanted Rei to be the same age so she could be a viable love interest. What do others think?

I don't know much of anything, but as far as i understand it, Rei 2 is biologically 4 years old, with her body having been artificially altered by NERV's technology.

Rei is both younger, older, and the same age as Shinji depending on the angle you decide to look on it.

-Younger
Rei is younger than Shinji because she has existed as Rei for less time than Shinji has existed as Shinji. Rei was born as Rei I in 2004, whereas Shinji was born around four years earlier. Adding all Rei's incarnations together would make her at most, ten years old. Even less if you just want to count the years of Rei's incarnation individually.

-Same age
Rei is according to the series file on her, and her looks, 14 years old or close enough to Shinji's age. Biologically she is the equivalent of a 14-year old outwardly. The official files and documents in the TV-series tells she is 14.

-Older
When you get down to it, Rei is just part of Lilith put in a human-like body. Lilith predates mankind by at least four billion years. Rei's soul is therefore much, much older than Shinji, or simply just older if we assume Shinji's soul has existed for a long time anyway.

Rei's a rather sewn together existence.

^ It's likely just derived from things Ritsuko has said;

Episode 4 wrote:

But we have to put piloting of Evas into the hands of 14-year-old children.

Episode 17 wrote:

However, we need those childrens of that kind, in order for all of us to survive.

I suppose it's possible that whatever people behind the scenes who were responsible for assisting Gendo in the creation of Rei I and her clones, might have also artificially accelerated her early physical development via radiation or some type of growth hormone regimen.

Then again, perhaps a series of significantly increased and dramatic growth spurts are just one of the side-effects resulting from splicing angelic-sourced genetic material into human DNA. Considering how quickly Sandalphon's metamorphosis took place during the Magmadiver episode, hatching in the volcano from its embryonic stage into a more fully formed entity, one might conclude that Rei's early infancy/childhood may have included events (to a somewhat lesser degree) which allowed her to mature at a much faster rate than the average human.

Though Rei doesn't have Angelic-sourced genetic material. Her non-Lilim genetic contribution (if any) came from a SoL, not an Angel, and the difference matters -- Lilith is as different from the Angels as we are. We can't assume much of anything about Rei based on what we see of the Angels.

That said, all sorts of wonky things could happen thanks to Lilith's contribution to Rei. She certainly seems to be capable of rapid growth when she cares to be. But I think it's simpler to assume Rei's development is the product of super science more than anything else.

If Rei is purely Yui's genes, then she looks like Yui just fine without being a "hybrid".

I'm not gonna argue about it. I explained my reasoning here, and if that's not enough for you it's not.