Well ignorance of new players is not an excuse. The first thing I did when I created my Klingon was discharge my 'Mission' BOs and replaced them with female Orion BOs, then purchased new level 1 abilities for each of them. Had more then enough merit/honor to spare.
Sorry, but I'm not talking Federation, I'm talking from the Klingon side.
First time Klingon players are at a disadvantage, not in gear but not being allowed to select their crew. And they won't know about the ability to go to a BO trainer and what skills would be best used in PvP.
My point is, Everyone has to go through that quest before they can even unlock Klingon to play. Therefore they should already know about going to the BO trainer before they can even make a Klingon.
So it doesn't matter if you don't care about the federation side. The devs gave the info about skills to you on a silver platter. Once you do go Klingon they even reinforce the importance of training skills by forcing you to do so, before you're allowed to fight in the ring.
As for knowing what skills are best for PvP, that goes with knowing your enemy and knowing your own play style. Since you have to get to know at least the first 4 levels, or at most the first 6 levels of the Federation side you should already have an idea about what skills you like. If you've PvPed in other games, you should definitely know to look over the available skills and equipment to start thinking about how each could be used and what could possibly counter it. Sure, someone that never PvP'd before will not think about this, in PvP terms, but unless they've never played a video game that has various skills, equipment, weapons, etc, they should still have at least a simple understanding of how the skills should work based on the skill descriptions.
Someone that is truly new to both PvP and gaming (in all it's forms) is going to have a very steep learning curve no matter how much info is provided to them. In fact too much info could even turn them off due to overload. In this case, jumping into PvP as quickly as possible without trying to first learn the game is just asking for trouble.
In any case, the info is available to those who actually look for it instead of just blindly dive in. This whole argument is liken to someone not figuring out how to set the clock on their VCR because they didn't bother reading the manual first then complaining that no-one showed them how to do it.
Lastly, everyone starts with 2 character slots and earns a 3rd one as soon as they unlock Klingon play. So if they make mistakes while learning the game they can easily start over and mail any non-bound gear from their old character to their new one once they figure out how they want their character to be. This will be a moot point soon enough once repecs are in place, provided those respecs include BOff powers.