A/N: Suits has been awesome at taking assumptions that both Harvey and Donna have about being together and breaking them down to pieces. Here are some of my thoughts about the same. Let me know what you guys think in the reviews!
In the beginning (13 years ago), Donna thought that Harvey was not ready to be emotionally involved and so, she instills the rule of not dating coworkers. There might have been some bad experiences in her past that led her there but the truth is that she probably did not think that Harvey was the guy she would be interested in for a serious relationship. So she decided not to go there and keep up the harmless flirting.
Harvey, from what I can ascertain from the flashbacks, thought that he could have both her friendship and sex with Donna until she told him he couldn't at the coffee shop. So he took the more steady relationship available to him because by that point, he already cared too much for her to risk having a relationship that could potentially end someday.
And so they went on. Donna would sometimes push/assist him with his slightly serious relationships. Some of it was because she hadn't completely accepted her feelings for him yet while some of it was because she subconsciously thought it would hurt less if she was aware and in control of the situation. This was especially noticeable when Zoe/Scottie arrive to shake things up. Both those relationships were meaningful to Harvey as he had history with these women, implying some level of seriousness. Zoe was a minor fling with the potential of becoming more. But Zoe was too heavy handed with her approach the first time and the circumstances prevented them from getting serious again because of her family issues (brother dying leaving her a niece to care for).
With Scottie, the history and his affection for her were pretty apparent, as they had been on/off since law school. The difference between Scottie and Donna was initially a slight technicality. Donna had always been on Harvey's side whereas Scottie was a direct competitor at work. This lay the foundation for the initial trust issues that Harvey and Scottie had, along with the fact that Scottie had proven that she had the ability to betray, which has always been a hard limit for Harvey. As they came together again, the Mike secret hung heavy between them. This was a consequence of his trust issues, though he eventually comes around in the end.
As we moved along in the storyline, we see Donna's place in Harvey's professional life being put to test as she shreds the fake memo and gets fired by Jessica for it. For the first time, she sees her relationship with Harvey in a different light when she sees him not fighting for her. On Harvey's side, it is about feeling betrayed for the second time by her and subconsciously, he is punishing her for it.
As they learn to move past it, we hit another major milestone moment, which is when they both confess their love to each other. For it to come out so naturally, they both must have individually realized it somewhere within the first few years of working at Pearson Hardman (or whatever the form was called at that point). To confess means that they were both subconsciously pushing the other to make a change but neither of them wanted to be the one to do it. It could be argued that Donna tried and failed because she wanted to be fought for. But she forgot the fact that they were not a traditional couple and Harvey would need prodding to be able to open up to her in that way. And that made her both angry and insecure and, so, in a fit, she decided to go work with Louis.
The panic attack situation with Harvey subsequently, was kind of obvious. It was the manifestation of his fears and feelings in a physical way as he shut down all his emotions. We keep hearing about people blaming Harvey for shutting people out but Donna did the same. When she left Harvey, as much as she tried, she also lost some semblance of trust in him to do what it takes. That later manifested to some of their conflicts about her COO position and decision-making in Seasons 7 and 8A, though part of it was also her kiss in 7A finale.
Finally I want to address the Paula and Thomas situation. As much as I hate Paula as a therapist, I think she was an essential character for Harvey's personal development. Being with her, with the shadow of Donna trailing them everywhere, was important for him. I don't begrudge him the emotional manipulation because that was cruel but we are all human and it is not hard to believe it possible. In order for him to start believing in the inevitability of his and Donna's relationship, it was a good first step. He is a character who needs to be convinced before he goes to do something. This was apparent in his mom's case too when he tried to reconcile with her multiple times but kept failing. There are some parallels there between him forgiving his mom and finally accepting his feelings for Donna. You need to keep chipping away at him.
As for Donna and Thomas, it was not as simple as Donna deciding to just move on from Harvey. That relationship was borne out of multiple reasons. After getting what she wanted professionally with a seemingly good relationship with Harvey, Donna was as fulfilled as a woman could be. But she was missing the steady care, companionship and affection of a lover. By that point, Harvey had pretty much bowed out from that position. And so Thomas happened. But as is always the case, Donna cannot separate the work and the personal ever in her life. Somewhere along the line, she absorbed the work family philosophy that Harvey lived by. And so, she found her worlds colliding and made choices she ended up regretting, which she realizes after talking to Alex. She finally accepts that she won't be able to let go of Harvey in this lifetime and carrying that around with her would fail all the romantic relationships she would try to build in the future.
Most characters in Season 8B chipped away at Harvey to get him to finally accept his love for Donna. It started with Gretchen who pointedly informed Harvey of Donna's date. Followed by her, Scottie made her point when she thanked him. And then, Robert and Alex, indicated the need of a partner. By this point, Harvey himself had realized how much he hated being on the fringes of Donna's life. Finally, it was Samantha who was the game-changer. Her thoughts weren't even about her need for a partner but she was mourning the loss of a mentor. But they led Harvey to acknowledge that he could have lost it all and the only thing he would have regretted is losing Donna.