A pretty solid new take on the show Anwar. It all works within itself - though the three Be'lannas thing might be hard to continue. Likewise the kes thing not so sure of.
The Tuvok interpretation is especially scary ass stuff - with Tim Russ well able to pull that off.
And the Neelix re-invention would have added a few other dimensions to his character as opposed to the joker in the pack.
I like how you plan to differentiate between Janeway and Chakotay as well as the ramifications for their working relationship. That would prove very dynamic and interesting in storyline ideas.
I however, wouldn't want Janeway to be promoted to Captain by fact of being the most senior officer left alive. I liked the fact she was the captain from the outset. Again with the post TOS choices for captains, Star Trek was making a statement through their choices. I think to start Janeway off as less would diminish that slightly. By all means maybe point out her lack of experience or maybe this was her first command but have her as captain.
I understand your approach is have Janeway prove herself as well as face difficulties within her own crew and the jostle for power initially with Chakotay.
I think the way around it though would be to beef up Chakotay's Fleet background. He is some sort of war hero from the Cardassain Wars who was outraged at the peace settlement and how their hard won victories were undermined by the colonists in the DMZ to be sold out by the Federation, thus turning him to the cause of the Maquis where he goes on to have an even bigger reputation for fighting the Cardies. This makes him a man of principles but also willing to do what is necessary to beat the enemy - including some unscrupulous acts by dent of his Maquis experience and seeing how Starfleet morals still allowed them to stand back and allow the Cardies to perpetrate their crimes.
As for the ship - whilst I'd like to see more of an ambassador class ship - I really liked the Intrepid class design.