Certainly an interesting idea, and I'd love to see some detailed suggestions. However, if/when they add the ranks of Admiral and Fleet Admiral, the skill point cap will likely go up. Even now, it's possible to have a good build in both areas. With a boosted skill cap, you could have an even better well-rounded build, so I'm not entirely sure a split is needed.
As they add more ranks they will also add more skills (at the very least they will add new ship skills if not more then that), these skills will also be most likely be more expensive skills. So if you spend into the top end you may very well suffer a net lose of skill points. Further as the space tree keeps climbing the ground skill has not. Adding another thing, like a ground rank, kills two birds with one stone alleviating this problem AND, giving players more to do, which is something I think everyone would enjoy.
I like the idea of ending competition between space and ground skills for the same pool of skill points. It's not clear that it will encourage more people to participate in ground combat or PVP, but it will stop penalizing people who like to do both. More participation really depends on Cryptic's revamp being fun, compelling, and more user friendly.
Honestly it would be a game mechanic, so I have no interest in Realism+Cannon argument. They have no meaning in the context of the game. Captain don't lead away teams, Vice Admirals certainly don't go any where near the enemy without a task force or at-least a squadron at their back. Also have you seen how many Vice admirals are running around? I mean how big is star fleet? I've heard of large officer corpe but come on.
However if it makes you feel better Realistically officers in the past have held ranks in other forces, look at Rome. Or from a more modern perspective officers hold equivalency ranks in those times that joint force operations occur. Canonically we know MACO exists so there isn't a reason your character couldn't hold a MACO rank and a standard rank.
We all have to deiced where our suspension of disbelief is, but in the end it is a game, and so it must have game mechanics.