Liquidisim: The starship skills such as Heavy Escort, do those carry thru to higher level ships such as fleet escort. If they apply only to t3 ships, then there is no point in having those skills come endgame.
Cryptic: There is hardly no point, though these skills currently become less useful in the endgame. However, we are in the process of changing this. All ship skills will grant some bonus to the ship above it. So an Assault Cruiser will benefit from Starship Captain, Cruiser Captain, Heavy Cruiser Captain, Exploration Cruiser Captain and Assault Cruiser Captain, but it will get the most benefit from Assault Cruiser Captain Skill. So if you want to maximize your Assault Cruiser, you will need all those skills. Note, the Assault Cruiser will not gain any benefit from the Star Cruiser Captain skill and vice-versa. The bonuses only affect ships upwards along the tree, not laterally.
I have already spent all my skill points (the cap is way too low!) and if tehy make this change before making a respec available, my character will be seriously gimped because I went science ship for tier 4 (Galaxy is no fun to fly). Furthermore, this will effectively end players ability to have the freedom to change ships at will...we'll be stuck in whatever ship we went line we went with back at level 11.
Common sense *SHOULD* dictate that they won't implement any major changes to skill trees without offering players a chance to re-do those trees. They may not necessarily implement unlimited respecs, but I SERIOUSLY doubt they'll make any changes to skill trees without resetting our skill points and letting us re-spec as we see fit.
From what i have read from little tid bits of info it seems the respec option is no where near rdy yet and is going to come later in in the year. So my hope would be a blanket skill point wipe out for all chars when something major happens like this so we can correct any problems that arises from important changes like this without the need for the respec feature to be active.
Tho thatís what i hope, in reality Iím depressed cus i doubt thatís what will happen and it will just get changed and those of us that did not put any points in the middle ship boxes will be screwed.