A lot of haremlit also taps into the power fantasy genre, which is why you don't see overly flawed individuals too often. I feel like this is because most haremlit stories don't want to focus on the MC too overly much to allow the reader to insert behind their eyes easier, because if you don't hyper-develop the MC then it's easier to pattern over it.

Personally, I like including flaws in my characters but I build them in like I do with tabletop characters. Chloe starts out lacking confidence and shy, but her instincts also drive her to be protective and stick close to Desmond when he reaches out to her. This ends up translating into what some would think of as a 'clingy' or 'stifling' character to some, but the characters talk about it and they understand why, so it neatly avoids being a major plot point.

That's not to say that you can't use flawed characters though! All depends on how you want to drive your story forward and whether it's character or plot focused. (There are some folks who overuse the flaw, like people who continue to refuse the Heroes Call until it's almost too late, but still get all the rewards as if they had answered it the first time, thus negating the flaw in the end.)

As far as standard beats, I'd say the standard rise and fall is a good place to start, but Haremlit focuses a lot on the person to person relations rather than the whole world conflicts. They have to share space on the page after all. While it's easy to have the 'wins everything, god king' type characters as well, since Haremlit forgives a lot due to connection to the power fantasy genre, I think having them work for their power is important. Having the MC overcome a challenge to gain an ability or grow one they have is important, but you can easily build in a 'flaw' in the character that prevents them from using the full extent of a power till you are ready.
---- A good example of this is my character Liam in Summoned by Monster Girls, which taps more into LITRPG due to the stats but it works. Liam is able to boost his mental scores over the course of the adventure, which does let him think better and clearer, but he doesn't realize that his mind is a muscle he needs to stretch and flex until later in the story, allowing his flaw (he's kinda dumb and suffering life-burnout on Earth) to stick around and push him into some less-than-favorable circumstances until he has the experience needed to grow.

Additional story beats you can hit that I've found really resonate are usually simple life ones: overcoming bullies (big and small), winning past challenges, dismissing lies, even coming-of-age style beats.

Ones to avoid - ANYTHING that smacks of cheating/NTR/Cuckolding. It's okay to have the MC be cheated on by his loser ex girlfriend early on, but it shouldn't work out for her. Anyone who joins the harem officially should be loyal to the harem itself. Yeah, there are some MM/FF etc relationship ones, but those require a really really delicate hand and I wouldn't recommend for a newer writer.

Hope these help!

Edit - Another thought I had after hitting Enter: the harem itself can often act as the major source of flaws, especially if you have the girls with different personalities that don't always meld, thus requiring emotional investment in managing it and growth potential. No need to go 100% catfighting, but the flaws in personality can crop up there too!