Oh come on, my dear Thomas, I never hid that I didn't like Chakotay's character and/or the idea of a Janeway/Chakotay's romance since the beginning (of my subscription on this forum), which earned me some quite violent reactions/recriminations, despite detailed explanation of the reasons that made me think so. Yes, Chakotay/Robert Beltran has got a charming smile but well, the physique of an individual, real or fictional never made anyone sympathetic or likeable as far as I am aware, right?! In fact, personally, it would rather tend to make me suspicious! <grin>
As for the Doctor, I will surely surprise you but I liked him although as a hologram, I didn't recognize him a legal recognition. But right the 4th season, producers/writers led by Robert Picardo changed his character in a grotesque character. From a doctor whose the tasks were classical, he became everything and anything. His omnipotence became for me annoying.
But what really bothered with these two characters is that both have 1) a lot of moralizing in them.
- Chakotay constantly questionned Janeway's decisions and/or physical/mental health, even if it was not always aloud -> I fairly question Chakotay's true motivations: to REALLY second her as any XO would do in that position or to take her seat, to show that he could do better than her, in taking control of Voyager (which proves to be bigger, more powerful & better equipped in armament level and crowded than his former vessel, the Val Jean).
- As for the Doctor, it was simple: he was convinced that he was better than everyone as an individual (although still being a common hologram), able to supplant everyone and in all fields.
-> isn't it ironic that the Doctor teached Seven how to be an individual while himself is unaware of what an individual is and how he behaves!
More I saw them in action, more I wondered if they didn't act/do worse than those they tried to supplant.
2) their lack of gratitude towards Janeway for what she gave to them: freedom to go and to be. Instead, they showed their propensity to betray her trust.
I must admit that it surprise me when you write that "Chakotay constantly questioned Janeway's decisions and/or physical/mental health, even if it was not always aloud" which you state as a reason for not liking him. Most of those who dislike and criticize Chakotay states that he was just Janeway's lapdog and never questioned her decisions.
Anyway, I must admit that I actually like Chakotay who is my second favorite in the series after Kes and who could have been the best First Officer ever in any Star Trek series if the writers hadn't wasted the character like they did in seasons 4-7.
However, I agree with your statements about The Doctor. He was much better in seasons 1-3. I never liked the idea of that mobile emitter. It changed the character for the worse. But I never liked the focus on Seven, The Doctor and Janeway in seasons 4-7 at the expense of the other characters.