Frontiershipping (Crystal/Emerald) - because of how expertly Kusaka has laid out the groundwork for this to happen along with subtly weaving very relevant themes into the development of their characters. To explicate what-in-de-heck I'm about, it is, firstly and almost paradoxically, because the pairing doesn't have the traditional sort of ship tease and related motifs that we've come to expect from anime/manga couples.
Everything that develops between them emotionally has a measure of realism and understated depth to it, as opposed to the more cartoonish semi-ST that transpires with MangaQuest through the series.
The very start of anything between them is depicted in the Emerald arc's flashback - not with the sort of fantastical beginnings present in Frantic (and even in Special to a degree), but with it dawning on Emerald how kind and dedicated to others Crystal is and him gaining a desire for self-improvement as a result of processing her awesome. The rest of the series continue to forge/show their bond in the background, away from the shonen manga typicalities, with scenes like her sewing his outfit, gestures like Emerald being entrusted with two of her party members, and (especially) their well-coordinated efforts in attempting to capture Jirachi, and following/depicting his growth as a character.
Of particular note in regards to that is a pair of scenes from HGSS and ORAS; the ones where either of them think about the other, wishing them happiness and safety, and they appear as mental images in the panel's backdrop. By virtue of their strongly-matching structure, it appears to me that the latter scene is quite likely a high note in Emerald's expressed character arc, if not its actual conclusion - Crystal and Emerald are equated with one another in that scene, as just two young teens who care about one another (I recognize that I may just be reading way too deeply into it, but, death of the author and all that).
By the time of ORAS, we see an Emerald that is both greatly matured and yet very recognizable - he is comfortable in his own skin enough to go without his heightening gadgets, emotionally comfortable enough to discuss his feelings with Ruby, even relatively heroic in his own right. In short, he has fully become Crystal's equal, and serves the same role among the Hoenn Pokedex Holders that Crystal does for the Johtrio.
It is because of all of this that they are my absolute OTP in PokeSpe, leagues ahead of the generic lineup - because theirs is a relationship based on maturity and close friendship, rather than trauma (as with Frantic) or the one needing to rescue the other (Special, Chosen) that also manages to be superficially cute (how many height-difference couples do you know where the guy is the shorter one?), one of the best-written relationship between any two characters in the series, which could very well transition into something mutually romantic (despite what the fandom's prevalent supply of thought-terminating cliches would have one believe, and shaft this one with "lol-sibling-on-her-part", something that is not and never has been as much as hinted at anywhere in the manga).
