ShinRaikdou

Kyouko is hands down the most boring girl in the game. Yuka is pretty easygoing on the outside, but suffers inside because of some factor. You have to rescue her from her misdeeds. If you get her bad end, it will surprise you, probably.

Aoi Isuzu?

yes, go to search>visual novel filters>Tags>Tags to exclude and writer there the tags you don't want to include.
https://vndb.org/v/all?q=&fil=tag_exc-214&rfil= as long as the tag exist you can either exclude it or include it on your search.
You can't add covers to the lists as far as I know i wish they was an option for that
On EGS you can do something similar by hovering your mouse on the titles and see the tittle covers, sadly it's all in japanese and a bit complex to use if you dont know the language but here is an example:
 http://erogamescape.dyndns.org/~ap2/ero/toukei_kaiseki/kensaku.php?category=game&word_category=name&word=narcissu&mode=normal
for tags:
http://erogamescape.dyndns.org/~ap2/ero/toukei_kaiseki/povlist.php?pov_id=42 
Be careful using the tags on EGS because it will spoil you the games, it doesnt seem to filter the tags like vndb
nope there isnt, maybe you can create one...(most of the time they will erase your new tag..)
it seems it's based on the numbers of votes and the general score too.

Hm, you made it sound like you wanted 2 girls.
Then, https://vndb.org/v1194
EDIT: Ah, didnt read  the last part.
I guess you can find a small conflict in that one, but it might not fit perfectly on that front. I get what you are asking for now

Well...

Really want a FD of noble works with Chiaki and Makoto.
--
And Miya from Amagami

But i know this was impossible in 15+ game...

Here's my take on Bunny Black from the 1st and 2nd game:
Darx, the protagonist rapes every girl who is being a mean bitch to him or harms his people. Furthermore, him having sex too much is actually relevant to the plot:
 
 
But he loves his wife and daughter far more than any girl. When he does it with others, he is fully focused to the girl and he does not compare them with others or thinks of sleeping with someone else.

Well...

Really want a FD of noble works with Chiaki and Makoto.
--
And Miya from Amagami

But i know this was impossible in 15+ game...

Aomi Isara
Kohinata Hayami

Hani Tsuma and its fandisc.
Happily ever afters, pregnancies and weddings.... EVERYWHERE!

... Akagoei isn't just comedy.  In fact, it isn't even mostly comedy.  It just has a main character whose hobbies are reading, driving serious people crazy, and doing whatever he feels like at any given moment regardless of what responsibilities he might have.

Hoshi Ori Yume Mirai
Hikoukigumo no Mukougawa (the redhead's route)
Akatsuki no Goei and its fandisc, Moe's route and after-story
 

The gameplay should be engaging enough and it's Eushully, so they never disappoint in that department. Akari's route is my favorite as well as Narumi. Like most Eushully games, it focuses on a heroine once you enter her route but the sidequests allows you to get h-scenes for side characters so if you don't want that, you can skip the scene or not recruit the optional characters altogether. 

You're probably right, Eushully games have so much content in the side routes that intentionally skipping that much content would be a real waste. It's also risky since skipping the side quests could lead to underleveling and make the main quest line too difficult. Though I still liked Servalwi's route a lot.
It's probably better to stick to Aselia and the soon to be released Seinarukana (which I'm eagerly awaiting myself). Can't recommend Yumina though - it was awful. 

Please don't recommend Eushully games. That's exactly not what OP asked for. In fact, I know people (myself somewhat included) who even kinda hate Eushully for making harem integral in every one of their games.
Even if it's theoretically possible, you don't play Kamidori without its sidequest. Why should you deliberately ignore the meat of the game? (Main romances are shit by the way...)
Soukoku no Arterial may be the least haremly Eushully game, but it has still some forced hentai-scenes. One in the common route, one in the light route, two in the human route and harem in the dark route. Some character sidestories have a hentai-scene included too (and again, you don't skip this. why should you deliberately skip part of the gameplay? that's not how you play an RPG).
 
To recommend something else: Brave Soul
I don't remember anything else though. Harem and Rape is essential to nearly all H-RPGs, haha.

I'm assuming you want something translated, apologies otherwise.
Seinarukana would probably count but it isn't out yet. By extension Aselia the Eternal would too. In the untranslated version of Aselia there is some rape (in fact there is a whole route dedicated about it) but that is all cut out for the censored translated version, which does not have any sex in it at all. 
Yumina the Ethereal might also be what you're looking for. The main character can have sex with other girls but it's all optional. And I do mean in the sense that you get a binary choice between if you want it or not. Not in the "well you don't have to do all the sidequests".
That's about all I can recommend with my limited knowledge. Hope it was to some use.