Found myself curious about something, so did a MaGOG search for the games with a bestselling rank worse than 1500, a popularity rank better than 500 and a rating of at least 4.0 out of at least 100 ratings, not including DLCs, removed, upcoming, in dev or demos. Came up with 9 games:
- Amid Evil (1831 vs. #270 @ 4.4)
- Hero-U: Rogue to Redemption (1691 vs. 493 @ 4.5)
- Iconoclasts (1516 vs. 366 @ 4.1)
- The Legend of Heroes: Trails of Cold Steel II (1686 vs. 124 @ 4.3)
- The Messenger (1651 vs. 323 @ 4.4)
- Overload (1530 vs. 379 @ 4.8)
- Parkitect (1751 vs. 247 @ 4.4)
- Pathologic 2 (1501 vs. 59 @ 4.6)
- Warhammer 40,000: Gladius - Relics of War (1924 vs. 111 @ 4.0)

Later edit, these get added if the ratings threshold is lowered to 50:
- Banner Saga 3 (1997 vs. 347 @ 4.0)
- Darksiders 3 Deluxe Edition (2085 vs. 193 @ 4.3)
- Divinity: Original Sin 2 - Eternal Edition (1737 vs. 92 @ 4.8)
- Druidstone: The Secret of the Menhir Forest (1505 vs. 168 @ 4.1)
- EXAPUNKS (2102 vs. 410 @ 4.5)
- Forager (1694 vs. 350 @ 4.0)
- Hypnospace Outlaw (2479 vs. 429 @ 4.3)
- Mary Skelter: Nightmares (1669 vs. 330 @ 4.4)
- Megaquarium (2002 vs. 163 @ 4.3)
- Shantae: Half-Genie Hero Ultimate Edition (2276 vs. 376 @ 4.4)
- SpellForce 3: Soul Harvest (1503 vs. 279 @ 4.1)
- SYNTHETIK: Legion Rising (1923 vs. 135 @ 4.4)
- Warhammer 40,000: Mechanicus - Omnissiah Edition (1615 vs. 82 @ 4.7)

Now the thresholds are rather arbitrary, but those are games that many check out, plenty like, but rather few buy. Any more probable reasons for it than too high prices / too poor or rare discounts (with the possible exception of D:OS2 EE and W4k:M OE for being special editions with other extras, but likely including D3 DE for including the DLCs)?

The Legend of Heroes: Trails of Cold Steel II IIRC, it is the fifth title in a series. Three in the first series, then the second in the second series of Legend of Heroes. This means that people may be interested, but will buy it if they already played 4 other titles before this one.

Pathologic 2. It is a sequel.

Warhammer 40,000: Gladius - Relics of War It is an evolution of Pandora: First Contact. Set in the world of Warhammer 40.000. People might want to check the other game first.

Despite the 2 in its title, it is not actually a sequel.

About the other 6, the names mean nothing to me...

So, the clearest case is for Legend of Heroes. Players of the previous titles in the series might be interested, while, at the same time, having so much backstory means playing four other titles first just to catch up with the story.

From that list, I own Amid Evil, Pathologic 2 and Iconoclasts. All three are great games and deserve to sell well. Pathologic 2 is very niche though, and its design isn't for everyone, so I get why it hasn't sold very well.

Amid Evil is a great old school shooter, much like Dusk. It's fast paced and has fantastic atmosphere and level design. I would definitely recommend it for anyone who liked Dusk or Ion Fury or the old Heretic games.

I haven't beaten Iconoclasts as yet, but it's very good so far, a colourful platformer with a great soundtrack and artstyle, and an involved story. I'm looking forward to finishing it.

The Messenger has been a freebie so that might have hurt sales. I am not sure that this is the case.

Hero U is definitely on this list for me. I'm interested in it because of its genre and pedigree, but I've never seen it at a price I'm willing to pay. I'm sure the developer would say that's me being a cheapskate, but in 2020 with literally hundreds of games in my backlog (many of them adventure games) it's just the reality of things.

Amid Evil is very much worth $20 though, in my opinion, and there aren't a TON of old school shooters out there like there are adventure games.

I think the problem with Pathologic 2 is the development model. They released it basically with 1 of 3 playable characters (Haruspex) and a promise that they'd add the other two (Bachelor & Changeling) "if it sold well". And doing that instantly causes a lot of people to hold back from buying it out of fear of being left with an unfinished game, which in turn translates to lower than expected sales and a "self-fulfilling prophecy". And the longer it goes on, the more likely people are to skip over it and buy something else that's "finished" before eventually forgetting about it and moving on altogether. It's also why I've grown to dislike Episodic style releases for "single piece" games in general (ie, stuff like Sam & Max Seasons 1-3 separate short stories actually make sense, but splitting games up into chunks due to lack of funds often discourages as many sales as it gains.

Yup, I want to play Pathologic 2, but I have no idea how much to pay for an "unfinished" game. So I wait for it to fall to ~10 Euro.

I'm never really sure how to perceive games sold under the slitherine label, most rank good to excellent on steam based on the public reviews. Especially when you take into consideration the numbers provided by steamcharts. Certainly not for moneygrabbing out there and maybe if you take into account sales from the slitherine site (wich comes accompanied with a steam key and gog ) and that warhammer games usually do seem to reach their public...
This one is not even that expensive for what it brings to the table. Personally i enjoy Gladius very much as a pretty enhanced turn based strategy game. Most people are accustomed to maybe civ since that was the comparrison i've seen most where gladius fails more or less content wise but it certainly manages to outshine civ on the combat level nice and easily.
Gamewise it is a pretty unforgiving game. Attacks from the ai opponents can be ruthless ( though again not that different from civ beyond or civ vi ) and the game does seem to ask of you to know at least a thing or two about strategy.
If you count in that a lot of wargamers prefer the reference to the real world then only the warhammer public remains which can be divided into the real timers and the turn basers with the real timed games being more of a seller then their tbs counterparts. I belief armageddon and sanctus reach did not reach very high sales either with armageddon being more expensive while i'm not really sure about sanctus reach.
the problem might be more that slitherine lacks a foothold in the general concensus which might be expected from a specialized developers company ( with also ties to some government branches )

edit
and they sell on apple ofc

Some of those games I do own here.

Hero-U was high priority because Rogue is my favorite typical fantasy class and I love the Quest for Glory series

Iconclasts I got because I like stories and games with Engineers or Mechanics as the protagonist, and enjoy Metroid style games

The Legend of Heroes: Trails of Cold Steel II I own for the Vita and haven't felt the need to double dip

The others just haven't made it high enough on my priorities to get yet.

Sure, here's some:

The Messenger treats GOG customers like second-class citizens by the devs not bothering to provide Achievements on GOG, yet they do provide Achievements for the exact same game on Steam.

When I see crap like that happen, I almost never buy games that partake in such shady behavior (with the exceptions for games that were released on GOG before GOG had Achievements on its platform, which certainly isn't the case with the Messenger).

And I'm sure there must be other GOG customers who do likewise for games that treat them unequally.

Plus, The Messenger was free on EGS, so there's no reason to buy it on GOG for anyone for anyone with an EGS account.

Hero-U is a great game that was pretty much ignored by reviewers when it came out.

It is a shame.

Not sure about the others, but for me AMID EVIL was one of the hidden gems in plain sight. I'm an avid FPS fan, owning pretty much every FPS game on GOG and completed vast majority of them. Really liked DUSK when it arrived here - and was routinely checking out AMID EVIL - price was a factor, but not major block - I'm happy to pay the price for quality product.

So if that wasn't a price - what was it? Somehow the screenshots and videos I've watched (e.g. Civvie review) really looked unappealing to me and I wasn't convinced I'll like the game. Enemies looked weird, weapons looks really weird and both not weird in a good way.

Still, I decided to give it a go and it's such a different experience from what I imagined! Not only I really liked AMID EVIL - it's quickly became one of my favorite FPSes of all time (I'm not kidding you). To the point where I paced myself to play no more than a level a week to keep enjoying the game for a longer time. I rarely replay games - but I'm confident I'll complete AMID EVIL again in the future.

The gameplay flows very smoothly and overall I was getting very strong Quake 1 vibes (yes, I know, not the first analogy you'll get from the screenshots) - the feeling of being in a strange realm, arcane dimension even ;-). Enemies that looked weird on the screenshots are fantastic in motion. Weapons I couldn't understand in videos are awesome - and not as weird as they looked, actually they're pretty practical and joy to use (you get your typical shotgun, chain gun, rocket launcher - they just look and feel different).

In my experience it was incredibly polished, beautiful and highly atmospheric game. Would I know that - I'd get it on day 1.

Overall if you're even remotely interested and respect classic FPS games like Quake - give it a go, I'm confident you'll love it.

For the sake of discussion, added 13 more to the OP, those that get added to the list when dropping the ratings threshold to 50. 3 of those are premium editions, but one includes DLCs so I'd include that too, if possibly not the other 2.
On the other hand, see that Hero-U and Pathologic 2 no longer show up in the list now, the former for dropping below #500 in popularity, the latter for rising above #1500 in sales.