I have a suggestion combined with a question.

Why not pool all the skill points...including Bridge Officer Skill points into one large pool and let the players decide where to allocate what and when and keep the pool continuing to grow like it does for the Bridge Officers?

Ultimately this would allow each player to allocate all their points as they see fit and allow them to max their character in all areas providing game play that is better rounded, and it would allow them to also decide how much they wanted to put on themselves and their bridge officers.

You must not like having 300k in space and 66k on the ground do you?

It's fine as it is until they up the level cap from 50 to 60 later this year.

Which invalidates the purpose of having skill points at all, other than temporarily inhibiting players as they level up. What you're suggesting not only makes Captain skill points or tree's irrelevant, but is already a problem as Bridge officer skill points do not have any tangible value. One of my characters has a pool of 3.5 million that, as things currently stand, will only continue to get larger.

Bridge Officer's in general, (like many other system's), need a redesign. The rarity scheme is clunky, inherent abilities are unintuitive, special traits should be added to all bridge officers or removed (and to the best of my knowledge, Leadership doesn't even work properly) and as already stated, BO skill points are nigh worthless.

No, not really. The decision to make someone invest in ground traits is arbitrary at best, and stubborn pride at worst. Despite the revamp, ground combat is still boring. Even if it weren't, about the only fathomable use those skills might have is in PvP. Yes, I know, I'll get someone screaming at me about how having 9 ranks in grenades saved an Elite Khitomer Accord ground run at some point, but I wouldn't know. I've run about three ground STF's, ever, and those were fleet runs, because few people give a hoot about ground combat enough to actually do them.

Wouldn't be entirely impossible, make the skill trees into actual skill trees so you can have the advanced energy weapons skill up to 9 without having the lower level at 9 as well.
And it wouldn't be hard to implement a scaling cost, say the first tree is at base cost and each new tree is at double the cost. So if you want to you want to max that 8th tree out each point will cost 256 times the first tree, soon soak up 3 million points

Quite frankly, I don't feel a need to defend my stance in this instance. You see, have limitations on the skill points that is less than being able to max out skills in all aspects of the tree undermines the ability of a player to be as well rounded as possible, and let's face it, a captain that isn't well rounded...well...they aren't a captain. I doubt if Janeway, Kirk, Picard, Sisko, or any other Captain in Starfleet ever got into their positions without training in all the fields that work on their ship, and if they did, they didn't do so without at least some basic training and understanding of those fields and how they could be used.

You kinda have to draw a line between balancing game play and the argument "you know Janeway wouldnt be happy if...".

A lot of MMO's with talent trees, do not allow you to max out ALL trees. It forces you to pick and choose what strengths you want your character to have and what weaknesses they have (unfilled talents). A lot of people already have the same gear, a lot of the same ships, and now you want them all to have the same talents and abilities too? That's like playing a game of chess where there are no pawns, but you can only choose between a bishop, rook and a knight.

You do raise a valid point.