Honestly, having a relationship grow between Tomoko and Komi-something wouldn't have been as crazy as it sounds. Yes, they tend to clash a lot, but we've seen that under all the vitriol they seem to have a weird sort of friendship where they're both fully aware of each other's entire personality. So it could possibly grow from there like it did with the other characters with little bits of comedy and serious character development sprinkled throughout.
To be fair though, the introduction of Yuri and Nemo was really for the better. They're like alternate universe versions of Tomoko. Nemo is the Tomoko who actually did good research in the whole "how to be popular" front and ended up lying her way to popularity. Yuri is Tomoko but without the eccentricities that make her interesting, both for the reader an in universe as we've seen people find Tomoko legitimately interesting.