In "Shattered", Chakotay breaks every JC shippers heart when he tells past Janeway there was a line they "never crossed" or something to that effect.
Just discovered this episode lately while sifting through the Seventh Season on CD's I bought some time ago and have been rewatching it quite a bit. Loved the story line and the interaction between Janeway and Chakotay as they navigated timelines with Janeway discovering to her astonishment/surprise and dismay in other instances (being stranded in the Delta Quadrant, Tuvok's death, etc.) the past/future events occurring in the Delta Quadrant and the characters she encounters she hasn't any idea of, including the fact that she and Chakotay would eventually come together as part of her crew, Chakotay, her lst officer. Every temporal segment as it unfolded was interesting, save for the out-of-place "Captain Proton" nonsense, which I couldn't stand even in other episodes.
After Chakotay inoculated Janeway so that he could take her through the different timelines on the ship as he needed assistance to bring the ship into temporal alignment, that interaction was very intimate with him holding her and speaking to her within inches of her face. They looked physically compatible together in that scene and it suggested intimacy to me via such. Yet, it was too early in the episode to even hint at an intimate relationship for Janeway only saw Chakotay as a Maquis terrorist to be arrested and brought to justice. Yet, as the episode unfolded Janeway softened her attitude towards him and one could see that she began to appreciate him in other ways to the point that towards the end of the episode after they had hatched a plan with Seven's help to bring the ship into temporal alignment, including learning that that angry woman, B'Elanna Torres, becomes her chief engineer and eventually marries Tom Paris, an ex con who becomes her navigator and assistant medic, an ex Borg drone becomes a member of her crew as well as the terrorist group the Maquis, Janeway becomes curious as to whether she and Chakotay have something between them other than he being her lst Officer. Love this scene and I thought was brilliantly acted by Kate Mulgrew. After she instructs the other members of the crew about the plan to return the ship to temporal alignment and sends them back to their respective parts of the ship in their temporal time line, she begins walking slowly towards the warp core with Chakotay, head down and rubbing her hands together, clearly uncomfortable with the question she's about to ask. Stopping before the warp core and standing very close to him she looks up at him and asks whether they have something together in the future with "a look of expectation that his response would be an affirmation". However, he responds, as you note, that they never crossed that line, which Janeway reacted with disappointment, but quickly asserted their professional relationship as captain and lst officer with a handshake. However, one can see by Janeway's body language and facial expression, she was hoping that the opposite was true. Outside of the episode Resolutions, that's the closest they ever came towards intimacy and why not from Janeway's perspective as Chakotay was a nice-looking guy and they evolved and bonded well as the episode unfolded.
Relationships in Star Trek.....didn't think Kira and Odo of DS9 were a couple at all, for Odo appeared more like her father than companion, nor Dax and Worf, nor Tom Paris and B'Elanna. Terry Farrell's Dax with Bashir would have been a better couple, as Bashir was after her from the opening of the series, interacted well with each other during the course of such and was admitted to by the 2nd Dax, Ezri (Nicole de Boer), in the seventh season, that he was the one, tho' they didn't mesh well, for it appeared that Bashir and Ezri were more like brother and sister than companions, as Bashir didn't react the same way towards her as he did affectionately towards Terry Farrell's Dax. Paris was forever admonishing B' about being harsh and hard to get along with. However, she was practically personable and friendly with Garrett Wang every time they had a scene together. They were the two that essentially broke the ice between the Starfleet crew and the Maquis in the opening two-parter and subsequent episodes in the lst and 2nd seasons. It could have naturally led to something but the writers saw not to develop such. Lastly, I thought Kira and DeMarr could've been something, tho' Kira hated the Cardassians due to the occupation, but both later became resisters after DeMarr's wife and kid were dismissed by the Founders/Dominion.