Normally I would agree with you, but since Mayuri (someone with very few genuine emotions) was affected by Szayel's words I can see Neliel being affected by Nnoitra's. Specifically if she finds herself being defeated by one of the more loud/battle loving Sternritters (like The Miracle), it wouldn't be unreasonable for her to think back on Nnoitra's words of "How does it feel to be beaten by that very same beast?" Also people have brought up that her relationship with Grimmjow is similar (though not exact) to her relationship with Nnoitra, so I believe a flash back could come out of that as well.
Mayuri and Szayelaporro are very much alike though; I can see why such words would affect Mayuri.
On the other hand, the emphasis was always that Nelliel was nothing like Nnoitra. She and Nnoitra were always at odds because she never understood him. Even as you say, Grimmjow has taken Nnoitra's place as being Nelliel's annoying little brother. The one thing that does connect Grimmjow and Nelliel is the damage Nnoitra has done to each of them. IMO rather than a flashback or other hallucination, it might be interesting for Nnoitra himself to reappear before him.
At the very least, Urahara really should explain how he was able to repair the damage to both of them. Such an explanation would of course have to mention Nnoitra in some way, you know, explain the peculiarities of damage caused by him, what needed to be done to patch it up, etc. We never did get a proper explanation of why breaking Nelliel's mask caused her to chibify when that didn't happen to any other Arrancar whose mask broke. Clearly Nnoitra's powers caused it by some means. The question of course is, what are his powers supposed to do?
Wasn't Hikifune the one who developed the mod soul? Either way I agree that Senjumaru's design is too close to Nnoitra's to be a coincidence. Hahaha Oh man can you imagine how odd (yet awesome) it would be for Nnoitra to be a secret war potential???!!!
Yes, Kirio is the one whose work led to the modsouls -- the idea of inserting power into another soul such that this soul would increase its power. Fwiw, if Senjumaru does have a clone around, Kirio probably does as well. I'd like to think the ladies collaborated on some project or other if they were both building weapons of mass destruction.
I would really like to see him as one of the remaining SWP. Kubo has to get that in soon, so perhaps it does connect to the issue of how Senjumaru knows Mayuri. If she built the original Ouken as a clone of herself, that should make said Ouken SWP-worthy. That is essentially the SK's main power, to bestow the Ouken power on others. A physical living Key would almost have to be part of the SK then, wouldn't it?
Kinda funny that it would make Nnoitra related to Yhwach.