These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Ensemble Darkhorse: Michael and Mrs Madrigal, who started out as secondary characters in Mary Ann's sub-plots before graduating to their own story lines. After the hiatus they each receive a book dedicated to their stories. Michael in particular is often cited as "the most beloved of Maupin's creations", and sometimes even "the most beloved gay character in fiction". Quite the honor!
Also D'orothea, whose return to the series was eagerly anticipated by a lot of fans, and seems to be much more popular than Mona, the character she was originally shown in relation to.
Ho Yay: Michael and Brian have their moments. Quite deliberately too: Brian's secure enough to walk down the street with his arm around his gay friend and it not be an issue.
Les Yay: Mary Ann and DeDe become extremely close in Further, with much Holding Hands or arm-squeezing. Towards the book's end, DeDe grabs Mary Ann's hand and kisses it.
Replacement Scrappy: Prue Giroux, Mona's replacement in Further. Stupid, selfish, and vaguely racist and homophobic, all in one package.
The "new generation" from the post-hiatus books (many of them the now-grown children of the "first generation") are young people facing realistic modern-day problems - essentially mirroring Mary Ann, Michael, Brian, Mona, DeDe and D'or from the first six books. Unsurprisingly, their chapters are generally less popular than the ongoing tales of the older crowd from the originals, though most reviewers seemed to think they were merely average rather than outright terrible.
The Scrappy: Mary Ann and Mona are less universally loved than a lot of the other characters, perhaps because they are shown becoming more selfish and self-absorbed as the series goes on. Contrasted with, say, Brian and DeDe, who go from being self-centred and rude to genuinely caring and likable, it's not hard to see why a bit of antipathy might set in.
Squick: The story Burke was investigating that gave him his amnesia? A cult of cannibals.
Strangled by the Red String: We never see the process by which Mary Ann and Brian fell in love, so their relationship in Further just seems to come out of nowhere.
Particularly jarring since, at the end of More, it's Brian and Mona who get together. Further might almost be seen to Retcon the situation, with Brian and Mary Ann an item, and no mention of Brian's history with Mona until Babycakes.
It's finally addressed in Sure of You: Mary Ann recalls how she drunkenly turned to Brian (who was still dating Mona at the time) for "comfort" the night Burke left for New York, and that their whole relationship kind of "drifted" from there, ending up with them getting married and adopting Shawna.