Janeway, Kim, and Tuvok were the only Starfleet Academy graduated senior officers alive when they entered the Delta Quadrant. Tuvok was promoted, and she couldn't promote herself.
Chakotay and Tom were given a commission, presumably with the last rank they held when they left or were kicked out of Starfleet, respectively. Torres got one, though she never finished the Academy.
There is no precedent in the books for giving a hologram a rank, so The Doctor couldn't have a one.
Neelix, Kes, and Seven were all civilians.
Harry Kim truly was shafted. With the exception of DS9, every Berman era series had a promotion shafted character.
TNG... Data. (Seriously, by the time of NEMESIS, every character got a permanent promotion except Picard and Beverly, and both understandably so. Geordi and Worf got it twice.)
VGR... Kim.
ENT... Mayweather, and arguably Hoshi. (Mayweather was probably the only senior officer who never did a bad thing on the job, and had the most space experience in the pilot. I say 'arguably' for Hoshi because she did have a couple black marks on her record, mostly from her Academy days and it looks like Archer might have had to pull a few strings to get her aboard at first. I will say shafted though because she proved herself well from the pilot to the end, and actually you can tell she had character growth despite the lack if writing. Credit to Linda Park for subtly giving a varied performance each season to show growth despite not actually receiving the scripts to do it with. She goes from screaming in terror in "FIGHT OR FLIGHT" to standing up to the Earth President in "TERRA PRIME". Great job!)