anyway! the way I see jongyu has morphed a bit since I first started shipping them. I think they're close (or close in theory) partially because they're the closest in age. when you think about it, age doesn't make much of a difference later in life, but when you're a teenager even one or two years changes everything. if I had been in onew's shoes it seems only logical to reach out to jonghyun, who's only 5 months younger, first, rather than the other three, who are 2-4 years younger.
they also have really similar attitudes/aspirations about music. they've both become reasonably good dancers, but they both entered sm because of singing--onew was in sm academy and jonghyun went to a music school before he dropped out and got a ged. with the exception of zhou mi, the people they trained with mostly specialized in dancing, so I can see them getting closer because of that as well--and it shows in the number of duets they've done over the years. they're also the two most interested in composing, so I can see them getting closer over that as well.
They have similar personalities, too, in a lot of ways. They’re both a little nerdy and weird, and I can see them having a lot of in-jokes or making geeky references that no one else in the band gets. They both can assert authority, seeing as how they act as “good cop” and “bad cop” with the rest of the band, but they seem to get seriously angry infrequently. There’s a lot of noise in shinee fandom about jonghyun being a douche, but I think that jonghyun, onew, and minho are the most inherently kind of the group/the ones with the least prickly personalities. That isn’t to say that taekey are douches, but I think they’re a little more aloof and awkward, particularly with new people. Jongyu are both funny, agreeable, smart, ambitious people that would have a pretty steady relationship (this is why a lot of people can’t ship them, because they’re basically baby animals with very little conflict).
that isn't to say that they're not different. onew's music taste skews a little older than jonghyun's--he likes jazz and trot and happily does musicals and even the opera solo for their concert. jonghyun is clearly a child of pop and r&b (see: his eternal devotion to wheesung and brown eyed soul). he went to rock of ages so he clearly supports onew, but I remember in one interview he said he had absolutely no desire to do a musical. but I could be totally making that up. onew used to be incredibly awkward on tv, but he's learned to adapt and appeal to a multitude of people and audiences. He fits in well with the established comedians. jonghyun knows how to appeal to shinee fans, he plays off of the other members pretty well, but you could never send jonghyun alone on a show. he's not someone with universal appeal like onew and he doesn't seem to really mind that either. He composes, he hangs with his heroes, he does smtb, he bangs sekyung-he’s got a lot of what he wants. but again, this is speculation and I could be completely wrong.
jonghyun’s a little more mischevious than onew and would hesitate much less about breaking rules if they got in his way-in an interview he gave a while before/maybe while he was trying to woo sekyung, he said “something has to explode for it to be fun” in regards to shinee’s clean reputation, and that’s something that, imo, onew would never say (at least not in public). Like I said, they’re both nice people, but I see jonghyun as having a small group of very close friends and onew being more willing to branch out/go drinking with people he’s just met. jonghyun doesn’t take teasing well, especially when it’s about his singing, and onew loves to tease and make jokes. Onew can drink much, much more than jonghyun, who gets really bad cases of asian glow. They’ve both been seen smoking but fandom seems to think that onew has quit. These might be sources of conflict, if you’re looking for them.
The tl;dr version is that jongyu are very similar losers with subtle differences that get along quite fabulously. if you have further questions go ahead and ask, and
undamage could probably go much more indepth than this.