Well this one is easy for me, though there are several great couples in the series--definitely
Jake/Cassie, my first ever OTP/ship, even before I knew the concept! Jake was by far my favorite character (and I admit I definitely had a literary crush on him!), and I liked Cassie as well (even if I'm the only one!), and I just loved their relationship, and was heartbroken when it ended in #54.
I was always more invested in their relationship than in any other pairing, I never cared as much for Rachel/Tobias, for whatever reason. As much as it pains me that they ended apart, I do love the tragedy that is Jake's character and J/C. And going back and re-reading the books and collecting J/C-related quotes, I still think they are a cute and well-matched pairing as well as a tragic one in the end. And not that it's a major factor, but I do think it's nice that they had an interracial pairing in the books as well, I can't really think of too many others in the book series I read and TV shows I watch...
I think my favorite moment is in #41, when Jake chooses saving Cassie over the world--if that doesn't show love, I don't know what does!
I do really love Elfangor/Loren as well though, it's a close second in terms of my favorite pairings, they were also pretty epic with their cross-species love and journeys and tragic end (I am an inveterate d00med shipper, it's in the genes I think, lol). And Dak/Aldea were epic as well...
Jake/Cassie was just too bland to get really interested in. I swear the only development they get past the first few books is 26, and anything else that may or may not have happened, happened offscreen so to speak.
Did you forget about "The Familiar", #41, which was pretty much ALL about Jake/Cassie? I'd say that Jake realizing he'd save Cassie over the world after his little AU test experience in which he saw her so changed as a Controller counts as a pretty significant "on-page" development in their relationship....
You also had plenty of other moments, like Jake and Cassie dancing and flirting more in #29, the various conflicts and growing tensions as Jake begins to lose it towards the end of the series, their temporary falling out over the Cube Incident, then their making up, and the proposal in #53 (which was perhaps a little random, but I can understand it, given Jake's deteriorating and desperate state at this point, eager to latch onto any promise of normalcy after the war), and of course their final disintegration as a pairing in #54.
There certainly were Jake/Cassie developments after #26, I wonder if perhaps as someone who considered J/C to be bland, you just might not remember them....