To be fair, being the first squadmate you acquire he sort of has to be the least useful and least interesting otherwise a player might not be as interesting in playing with some of the others.
It's sort of compounded by the fact that by the time that you've levelled up to the point where he might actually be of some use, you'll have a whole slew of much more interesting and powerful characters and will have probably forgotten he's even there.
Another factor may have been that his loyalty mission was so dull and disconnected with the rest of the plot. Plus of course the fact that Miranda, Tali, Thane, Samara and (I suppose) Legion also all had loyalty missions that involved family members didn't help much either. I mean, who cares that his father turned out to be a power mad castaway/rapist? What did that add to Jacob's character exactly?
In hindsight, perhaps something involving his time in the Alliance corsairs might have provided much more fertile basis for story telling, filling out his back story, adding depth and a perhaps a bit of a character arc.
On top of that I get the impression there was supposed to be a rivalry between Jacob and Thane similar to the Jack/Miranda & Tali/Legion confrontations that was ultimately cut out of the game (I think Grunt and Mordin were supposed to have one too.)
Add all of this up and Jacob just became a bit of a non-entity. I mean what exactly was his job on the Normandy anyway and why did it mean he had to spend all his time alone in the armoury?
As for the paramour storyline...no sorry. I tried with one of my femsheps but his dialogue just creeped me out and she purposely got him killed on the suicide mission.