Tom got demoted for violating the damn prime directive, and gets his rank back a year later.
I know... and there was no good reason to deny Kim his promotion at that stage.
However, Janeway gave a field commission to Paris to Lt. in Caretaker Pt. 2. So that means he was probably an ensign by the time he left the academy and caused that accident because those were special circumstances.
Oh and even though he was demoted and promoted again in just 1 year, I seem to recall he did NOT advance in rank AFTER coming back from the DQ. On LD, he was still a Lt (and that show takes place years after VOY ended).
So, his 1 year demotion notwithstanding, Pairs has been a Lt for longer than Kim has been an Ensign (that we know of).
Janeway slept with an alien and always ignored ALL the regulations!
Did she though?
Kasshik of the DeVore might have been her passerby romance - but beyond mere kissing, I don't recall that they were sexually intimate (and Janeway would have had the sensibility to scan them while their inspection teams were onboard with internal sensors to make sure they weren't posing a bio threat - or the DeVore would have done that beforehand as I'm pretty sure they would also be hesitant about boarding a vessel that carries aliens which could pose a bio threat to their species).
The second one was when the crew was kidnapped and got their memories altered... so she was really acting without any real awareness of her own and the local doctors probably made sure that different species mixing wasn't an issue on a biological level.
Kim broke regulations because he knowingly engaged in sex with another alien without anyone's permission or knowledge and the Doctor didn't have any data on Varro biology.
And just to reiterate... I'm not saying that his lack of advancement was right... I'm just trying to find some kind of in-universe explanation that would have justified it.
He may have 'exceeded' Janeway's expectations in "Twisted", but lets be realistic, Kim was at the very start of his career and that would be considered a 'step in the right direction' (plus, the 'original' Kim did die in 'Deadlock' and got replaced with his duplicate - perhaps that played a part?)... and despite on how well he performed then, we did get a dialogue in "Demon" episode that he was still considered by Paris to be 'fairly green' in the early years.
Also, correct me if I'm wrong, but no other VOY member beyond Tuvok and Paris received promotions (sans Torres who had to be given a high ranking position as chief engineer - and she also didn't advance in rank that we know of - I suspect that both Torres and Paris would have ended up waiting longer before they advanced in rank due to how they got it in the first place - not that they hadn't earned them, but still...).
Chakotay was already at a rank of Commander before he joined the Maqui... Janeway simply reinstated his authority as they both agreed to function as a SF crew and thanks to Prodigy we know he was promoted to Captain by SF after they returned to the AQ.
Only Janeway, Tuvok and Chakotay seemed to have (thus far) been promoted in-universe... we know from LD that Paris did not advance in rank (not sure about Torres - and would she want or need to?).
Kim probably would have accepted a fast track to Lt. Commander (Janeway likely stuck up for him as a way to maybe 'apologize' for not promoting him sooner).
I mean, with Kim not being promoted during his service on VOY... no one else on the ship got promoted either... sans Tuvok (and he ended up in Starfleet a SECOND time and we don't know how long he's held his ranks before he progressed further - though we know he advanced to Admiralty by the time of Pic S3).
put some pics and episode info on MB 
