a) I believe this was included to further differentiate the classes. I find myself really having to strain to decide which skill to take, since I get so few level III skills.... but I like that. It means I'm defining a role. I can always change out which BO is at a station if I want to change abilities.
It is, however, nice to know that the best Science skills are for SCIENCE SHIPS. This will keep Escorts from being THE uber PvP ship, and Cruisers being THE uber PvE ship. You can use the tier I and II skills from the other professions, but if you want ANY of the best, you need to switch to a ship with the appropriate equipment.
b) See above. It promotes differentiation of ship classes. It also means that you can't have ALL of the tier III abilities for your class at the same time--because they all crowd into the top two ranks, so you've got to choose which you have equipped at any given time.
c) As designed, I'm sure. If you could train ANY of them, why choose a class? Your class determines which high-level skills YOU will have that the other guy WON'T. Differentiation. An engineer in a Science vessel SHOULDN'T be as "science-y" as a Science officer in a science vessel.... but if he can train all of the best tier III skills, he would be.
d) Also a good thing. Otherwise, you'd be able to bypass the class differentiation. As an Engineer, I can't train my BO for Viral Matrix III. This is because it's not in my specialization to do so. But if I could just get a BO with Viral Matrix III from my Science buddy, then I might as well just be able to train it myself.
Your concerns, while broken into 4 categories, really come down to 2:
A and B are concerns with what skills are available because of the SHIP CLASS.
C and D are concerns with what skills are available because of the PLAYER CLASS.
Both categories are in place so that a player functions BEST in the ship that matches their class, even though they still have the option of flying others for other benefits. As an Engineer, I would be greatly offended if a Tactical officer could have all the best stuff I have while flying a cruiser, and now my only "advantage" is class skills (Woo. Nadion Inversion.).
Players and ships should differ in more than just 4 class-related skills.
1. I agree that my concerns are essentially in two categories, which is why my discussions frequently grouped them the same way you did.
2. First, your argument to point c) is, in fact, my point. I'm not sure if you missed it, but I stated in my post that I wouldn't change the fact that a class can't cross-train tier III skills.
3. Your argument against d) is kind of spurious. It isn't the same as just training a skill myself, because it would require an investment that I would otherwise make elsewhere. The fact that my buddy made a different investment means that the system would PROMOTE differentiation. Also, it would promote inter-player communication and trade.
And, if implemented with a cost system, like a cooldown, there would be a limit on the market, thus, again, not making it the same as training it up myself.
4. I agree that points a) and b) promote differentiation, to a certain extent -- as I mentioned in my post. However, both in conjunction limit players unnecessarily. There are already skills that certain ships cannot use, which I'm fine with -- that totally makes sense. Making it so that higher levels of skills people can already use are also limited is redundant, confusing, and overly-restricts players. It also means that there would only be reason to get 9/9 in THREE skills for your captain, which, in a sense, limits a certain type of differentiation.
Your argument actually doesn't make sense. How would allowing a science vessel to use a stronger version of a skill they could already access allowing them to surpass another ship? If you want to use really cool skills, you STILL NEED TO SWITCH SHIPS, because skills are limited to certain ranks. However, if you can already use a skill, you should be able to train it up to the tier III version with enough work and investment. It allows for more investment, more work, and more differentiation.
Also, I want to note that you seemed to misunderstand me. Skills are limited by rank, and I suggest they stay that way. Viral Matrix wouldn't be a Lt. or Ensign skill, and therefore wouldn't be able to be used by anything but a Science vessel. So Science vessels are still different from Escorts, etc.