The Doctor and Seven makes no sense, for the following reasons:
-We know the doctor is infatuated with Seven. This is consistently shown
What is also consistently shown is that Seven does not share those feelings. She considers him a friend, and has no romantic interest in him/doesn't see him that way
-He's also her doctor, personal mechanic, and part time psychotherapist. Let's leave "doctor dating his own patients" to Bashir
-Lastly, Seven has lost 20 years of her life. If she gets into a relationship at all, she deserves it to be with a person, and not a simulation of a person
Janeway and Chakotay doesn't work for the following reasons:
-Janeway has consistently shown that she is not willing to date someone in her chain of command, just like Picard, Kirk, etc.
-workplace relationships often have negative consequences, even worse when it's in a military direct chain of command with no ability for anyone to transfer. She's making a sacrifice for the good of the ship, but it's hers to make.
Reasons Seven and Chakotay makes perfect sense.
-Chakotay is a romantic, lonely, and I cannot see him ever turning her down. Plus, she's a civilian, so he doesn't have to worry necessarily about dating a subordinate.
-In "Human Error," Seven(who has been looking to try a relationship since season 5) chooses Chakotay as the most compatible partner for her on the ship. She creates a holoChakotay to be as close to the real thing as possible, so she can experiment with dating him before trying the real thing. She ends up falling in love with him. From then it was inevitable that she would eventually work up the courage to approach him. By the time of Endgame, some time has passed, and Seven and Chakotay are just in the very earliest stages of a potential relationship. They've been on one or two official dates, that seemingly went well.
Compare this to Worf and Deanna, who out of nowhere suddenly sleep together and begin dating. I'm also fine with not having 3 seasons of "will they, won't they" That stuff isn't necessary except for in soap operas and sitcoms.