Grunt and miranda are kind of the same character. All of the character explorations that happen with grunt also happen with miranda. They tell the same basic story and it lessens both of their characters in context. The clone krogan would make an interesting foil to miranda; he was made to be perfect, failed, and was rejected. His journey to self actualization compared to with Miranda's would tell a really interesting story.

How I picture it going is you meet him and he agrees to guide you to the lab. You have another chat with him after you fight through the horde of released krogan where he expresses a discomfort he cant quite word about having to kill them. You can ask if he knew them/cared about them and he'll respond that hes not supposed to. They're nothing, imperfect, like him. Maybe he should have stayed by the door and died like them. Shepard can leave him here or ask him to continue to take them to lab.

Once they reach the lab the clone will be sort of in awe of grunt in the tank. That's the perfect krogan. The one the other clones died for. The one he was thrown away for. Hes perfect. Okeer will refer to the clone as refuse or garbage and question why shepard brought him, referencing how shepard had no issue killing the krogan clones on virmire. Everything else plays out the same way until jadore releases the neurotoxin, killing grunt and okeer. Clone krogan is horrified to find them dead, because they were perfect. They had purpose, they're supposed to live and hes supposed to die. Shepard will ask him to join up, offer him purpose or revenge or something.

On the ship, clone krogan will have a few conversations with shepard about what it means to be a person. This has the opportunity to give shepard the chance to explore whether they think they're still them, and flesh out any anxieties about having a control chip in their head. Clone krogan knows that he was brainwashed and has some feelings about it. How shepard reacts to this is a good chance to give them more personality. Less focus on what it means to be krogan (violence/revenge for grunt. He gets happy about that memory of a turian getting torn apart. While in context, grunts anger at what happened to the krogan is totally justified, it feels weird having it only center around getting bloody revenge) and more on what it means to be an individual with autonomy. Shepard and clone krogan have a few parallels I'd love to see explored as well; both built for a purpose they had no say in and both ejected before they were finished.

His loyalty mission remains the same as grunts. No need to change it. At the end of this mission he chooses a name. Completing the rite is the first thing he did for himself, it connected him to shepard through them being his krantt and defending him to the other krogan, it allowed him to connect to his culture, and it gave him a place in society. I dont know what name he would pick yet, maybe grunt still. (I like the patriarch mission where you can be the old krogan's krantt. The genophage storyline talks a lot about how cultures die not just through physical deaths but because people in power prevent rituals and behaviors that are important from being practiced. Giving clone krogan a chance to do this is a chance to help preserve krogan culture. Also with grunt. I just like this bit). Afterwards, wrex will pull shepard aside and say that hes a real krogan. Then he'll ask if that means the krogan on virmire could have been real krogan too. If he helped kill his people back there if shepard was wrong to end them. Shepard might reply that they were being controlled by saren and that if they'd been left alive they never would have been able to stop sovereign. Then maybe a paragon choice to add that it isnt an excuse though. Those krogan didnt deserve to be controlled by saren and they didnt deserve to die. The krogan people shouldnt be used as tools by anyone. Wrex will respond that if shepard doesnt see them as tools, would they be ok of clone krogan stayed on tuchanka and shepard will reply it's their choice. If they dont use this dialogue wrex will imply that shepard is using the clone krogan the same way saren was using his army and he'll be less trusting of shepard in the 3rd game.

Some squad interactions I would love to see with him would include:

Discussing what makes a person a person rather than a tool with EDI.

Discuss what it means to have a soul with Legion. Also possibly, what it's like to kill your own people for not thinking the same way you do (okeers other clones/the heretics).

What it means to be perfect with miranda (different depending on if they're loyalty missions are complete. Prior to both their loyalty missions this conversation results in both miranda and clone krogan agreeing that hes essentially trash and he will wonder about what grunt would have been like in his place. If his is complete and hers isnt, he stands up to her dismissal and they fight. If hers is complete and his isnt, she tries to tell him that perfection isnt what matters connection is and he dismisses her, wondering what grunt would have done in his place. If they're both complete they talk about how they arent defined by what they are but by who they become and who they love).

What it takes to make your own life once your free from the expectations of your authority figures with thane (different depending on if thanes loyalty mission is complete).

A discussion with jack about lost childhoods and stolen identities.

Mordin and him talk about the morality of the genophage (Mordin doubts his actions but doubles down anyway and clone krogan becomes enraged. This leads to a confrontation where shepard either has to take sides and lose loyalty or pass a morality check.)

Eventually I'd like to think that he looks virmire up or asks about it and learns that shepard killed all the clones there. If this conversation happens before his loyalty mission he'll be surprised shepard let him live. If its after his loyalty mission he'll get mad. He'll insist that if hes a person, then they could have been people too given half a chance. I'm not sure how shepard would respond in this conversation but the constant abuse krogan suffer at the hands of other races makes me incredibly sad and I need someone other than wrex to acknowledge it.

I can also see him being a lot more wary of accepted truths about krogan, told from both the krogan perspective and the citadel races. He's unlearned the brainwashing from okeer and might have views more similar to Eves from the 3rd game.

In the 3rd game everything remains the same. He shows up as a fully actualized person leading a squad. It's beautiful. I cry because I am so proud of him. The only possible difference I could see would be that he might support saving the queen. He might see them less as old enemies and more as another race that got fucked over by the short sightedness and racism of the council. He believes that everyone deserves the chance to have their shot, no matter who or what they are. It's hard for a person or a species to self actualize when they're constantly being abused or living under threat. This perspective might extend to the geth if he survives the rachni.