I think that it is because Jacob has such an intense personality and there really isn't much room for the character to become multi-dimensional. Take Miranda for example, she is a strong personality that reveals underlying insecurities regarding her genetic engineering. She overcompensates for that insecurity with severity toward others and as you shore up those personal weaknesses, she opens up. Jack is another example of this type of personality. You get the sense that there is more to Jacob, but he never gets to reveal that side of himself.
Arguably, a game is a poor medium for character exposition. However, reveals can be done through extended dialog between the PC and the squadie (hint, hint, hint), banter between team members, personnel files, meetings with people who have known/worked with them before, all help to flesh out an NPC. In fact, one of the more enjoyable ways of gaining an insight into the NPC's minds came from emails sent to Shepard. One of the more memorable emails was regarding Garrus sent by the wife of one of his dead teammates. I only wish that I could have followed up on some of the mails because that would have been an ideal method of character revelation, bonding, and development.
In a sense, Jacob was pushed to the back burner in the story. His character has honor, integrity, and hope, but these are rarely showcased. As a result, most players just glossed over him because they found some of the other characters more interesting. In fact, DLC could have been a great tool for further exploration of characters like Jacob. Although I really enjoyed and appreciated Overlord, I was disappointed that we didn't see more of a reaction by Miranda to the horrific events portrayed there. Given her reaction to the destruction of the Collector base, I would think that she would have had a real issue with Archer's handicapped brother being conscripted as a guinea pig in an experiment on the Geth. Unfortunately, this wasn't done.
As the gaming medium moves more towards the cinematic, character development becomes more important because the gamer's use of his imagination decreases. Where once games like Zork required as much imagination as you could muster, today's cinematic sequences, professionally voice acted NPCs, and fully developed story lines leaves little to the imagination. Motion capture expresses even more of the NPC's character by giving the player facial expressions to read greatly enhancing the VA's performance.
I think that gamers pick up on this intuitively, if not intellectually, and that is why they so often request further character development, better dialog options, and enhanced romance. In essence, the gamer has transitioned from player to a participating member of the cast and this brings us back to Jacob. As a member of the cast of ME2, do you spend your efforts on trying to squeeze blood out of a turnip or are you going to spend your efforts where you will get more out of them?
Essentially, that is what I think happened to Jacob and I hope that ME3 does the character justice.