I think the thing is, if you're going to make a pairing a large part of a fanfic that is ultimately about something else, it needs to be either canon or well-developed within the course of the fanfic. Otherwise you risk mischaracterization which damages the rest of your fanfic. Actually, this pretty much goes for all long fanfiction, whether or not it's romance/pairing-centric.
For instance. "Ripple Effect" is not ultimately about pairings, but LeeSaku forms a large part of the fanfic. Unfortunately, it's not developed beyond "Lee and Sakura are madly in love and are precious and important to each other in a romantic fashion." Since canonically, the relationship between the two is ultimately platonic (on Sakura's side at the very least), this eventually starts damaging the characterization of Team 7, especially with the canon Sasu<Saku having been completely removed from the writing, again without development or explanation.
I'd go on about long fanfic that does follow these rules I just randomly made up, but I haven't actually read any (unless you count "House of Leaves," which doesn't actually seem to have any pairings yet). Whoops. So instead I'll talk about my own fanfiction.
"Forest for the Trees" was ultimately about Kakashi's brokenness, with a significant focus on KakaRin. Kaka<Rin is strongly implied as canon; most of the fanfic was dedicated to developing Kaka>Rin.
"Spiral Out," not being romance-centric to the degree "Forest" was, is more complicated. Naru<Hina and Sasu<Saku both play a large role in the story, but these are firmly canon. Naru>Hina will be developed within the fic towards the end; Sasu>Saku will be subtle and kept mostly in undertones. TemaShika plays a background role in the story, but besides being implied potential canon, it's not one of the driving forces. ShikaIno will probably have more time devoted to developing it in the fic than any other two-sided pairing.
The rest of the relationships I'll be working on or referring to will remain platonic.