Eh.. I'm happy with the system as is. Is it perfect, No. But it does create challenges. I've yet to come accross any mission that I could not overcome.
I'm a Tactical/Cruiser type and find it to be fun. I had a slight disapointment when I could train my BO in HY3 but could not use it, but I make do. I picked up a BO from the exchange for about 200k with Reverse Shield Polarity III and have been able to find the ones that I like as well.
I just hope that everyone knows what they are asking for. The current system works, and many people are happy with it. I'm concerned that the loud few will bring about changes that the quiet and content (majority?) will not be happy with.
In summary...be careful what you wish for.
Well, the current system is "incomplete". Many such aspects of the game are, but in this particular case we're supposed to be able to trade bridge officers we've trained. Although the intention has always been there, that system simply isn't in place yet. Apparently it's being worked on and is coming, however.
In the end that means a player won't be penalized for not matching class and ship type. And why should they? Unless you happen to be one of the minority who frequents the forum there is absolutely no information available on the synergy between career and ship role. No hints, no warnings.. and I'm sure many a player comes into this game for the first time with a desire to captain a specific type of vessel. Yet we pick our career before we even start playing the game with only a short in-game blurb vaguely describing to us what that choice means, much less how it interacts with your choice of vessel.
I say "won't be penalized", but I should really be saying "won't be further penalized than they already are". Are you aware that, as a tactical officer, you're given access to a series of space skills that can only be improved by investing points in an area that has absolutely nothing to do with your chosen vessel? For example, your "Attack Pattern Alpha" ability is improved by investing points in the "Escort" and "Heavy Escort" skill blocks. Yet, as you are a cruiser captain I'm sure you would rather be spending points in the "Cruiser" and "Heavy Cruiser" sections instead. You're faced with a choice of either gimping your special abilities or spreading your points around thinly enough to cover more skills than an Engineer in a Cruiser or Tactical in an Escort would have to do.
So, you're already penalized. I don't think further penalization is necessary by making it so our Bridge Officers don't have access to nearly 50 rank 3 skills. I'm all too happy to see that's being fixed. Or rather, that a feature the design was built around (trading officers) is being completed.