That was a really good analysis, tykobrian. Very interesting points you bring up.

As much as I respect your point of view, some things you write are far fetched to me. Where and when do you see them in the show. For exemple :

tykobrian wrote:

When John Marries Mary and thus rejects him as a romantic partner, Sherlock finally knows what it feels like to be rejected by someone you love completely and hopelessly. The way I see it Sherlock calling Molly to help him (TEH) with his cases was more about himself. John has told him to f*** off. He’s ravaged by that rejection, just like Molly’s always is. So it’s interesting that he chooses to include Molly in his life in a new way just then. He suddenly understands what it would mean to get the attention of someone he loves, and he’s finally behaving with some level of empathy towards Molly. For once, they’re in the same boat.

But, I agree with you that Sherlock Holmes is uncomfortable with Molly, as long as she expresses (even unvoiced) feelings.
Holmes is comfortable with dealing with adversaries, but Molly doesn't lie, doesn't fake or pretend and Holmes doesn't know how to cope with genuineness (he doesn't either know how to cope with Watson's genuineness, he seems to be more at ease with bickering) 
You can see thet when she asks him direct questions ( do you think i'm a drunk?) or statement ( you could at least say "thank you")....

Besides, I think she was quite professionnal, when Holmes and Molly have been working together. Self conscious, but professionnal. For the first time, I saw a real sign of their friendship (jokes, knowing smiles)

Maybe inviting her for dinner and take it back her immediatlely was a subtile way to reinforce their "friendship but nothing else" ( as in " I'm enough of your friend to share a dinner with you, but we won't do it as I don't want to interfere/have a part in your love life")

I never got a good chance to look at that.  Add that to her look of concern as she sees Sherlock leave before returning her attention to Tom to try and be enthusiastic about dancing with her, and she definitely cannot put her feelings for him behind her.  You could kind of tell from when we first see Tom that he's a replacement for Sherlock.

I understand quite well why she sort of declines the invitation. This day has been work, work with Sherlock, but still work. An invitation for dinner would cross the threshold into something more private. They never even had coffee or tea together when she was single and now she is in a relationship. Maybe she does not trust herself enough or does not want to build up false hopes. I think she draws a line for what she thinks is her own good. 

That might be a reasonable explanation for real people, but Molly herself suggested "dinner" when she first came into Sherlock's flat - she wasn't expecting to be invited to work with him!

 

I just want Molly to get with Lestrade so she can be happy and finally get over her interest in Sherock (which is clearly going nowhere).

Brilliant. Count me in. 

Just want to pick up this topic, because I find Sherlock's and Molly's interaction VERY fascinating.
Sherlock, as we see him in seriesn 3, has developed a lot, he seems much more mature in a certain kind of way. I think, he asked Molly to join him for two different reasons:
a) He wanted a substitute for John, because he hadn't come.
b) As he tells Molly later, he wanted to say thank you.
So far, so good. But this scene in staircase is so full of ... tense and awkwardness. When Molly realizes that Sherlock really wants to invite her for dinner, he starts talking about his fianceé. Why does she do that? I think it's kind of a protection. Molly has moved on during the 2 years of Sherlock's absence. She has found a new boyfriend and obviously it is serious (although we know at the end of TEH that he looks exactly the same like Sherlock - gee, love this scene :-)). She reveals that she has a normal life and that she is happy. Again, why does she do this? Because she exactly knows that Sherlock can again be "dangerous" for her in a romantic way - and that is somethig she wants to avoid! She doesn't want to go through this unhappy I-love-you-but-you-don't-love-me-thing again! And that is exactly the point when Sherlock alludes to her ring. He respects that she retreats. I can't say if he really had something in mind like dating or even kissing her (but don't forget, Sherlock had enough time to develop during the past 2 yeras, just generally spoken), but I believe to see in his eyes that he was about to DO something in the staircase facing Molly. And then he kisses her on the cheek. Would he have kissed her at that moment if she hadn't told him about her boyfriend and everything???

Vhanja wrote:

I see it a bit differently. I don't think Sherlock has ever had any romantic interest in Molly. But as you said, he has developed a lot over the last seasons. So while he in S1 and (partly) S2 was cruel and dismissive of her, he learned to respect her and not just see her as a tool to manipulate whenever he needeed something in the morgue.

Absolutely right. I don't think either that Sherlock has (had) any romantic feelings for Molly (so far). Definately not during sreies 1 and 2. I'm not sure that he even realized that he had a crush on him (at least as far as series 1 is concerned).
But I'm not so sure anymore about this staircase scene ...

Vhanja wrote:

What I see in the staircase is him treating her with that kindness and respect. I don't think the "fish and chips" request was meant to be a date, but to show friendliness and kindness. As he said himself - his way of saying thank you for everything she's done.

But I see her response the same as you - she knows that it will be dangerous for her to say yes, it will lead her straight back into her crush (the one she has never gotten over really). I think she is trying to tell him that she is doing fine, that she is over him (which she isn't). 

Interestingly enough, the man who can't understand sentiment realises all of this (I believe) when he says "But you can't do this again, can you?". He has indeed come a long way.

Yeah, and that's so fascinating. To me it means he would have liked her to join him more often during his investigations, but he is suddenly fully aware that she can't do this because she is still in love with him, but doesn't want to be anymore. And he respects that! WOW! I think their relationship has come very far.
I still consider it possible that they both will develop a ceratin kind of (romantic) relationship. Of course not a daily one with him giving her flowers or going to the thatre and what else, but I'm pretty sure there will be a certain kind of development.