Ok guys, I understand this will be VERY subjective as not to break lore, but these are mere ideas.
I feel there needs to be choice in choosing a ship within it's class. It's great that we can choose the ships we like and captain them to our heart's, knowing it is no better or worse than any other in it's respective class. BUT what if your decision was made a little more though provoking by altering a few stats to make you consider your choice, as apposed to choosing your favourite or what looks good.
As an example here's the Olympic, Hope, Horizon Science class vessels.
Say that the Olympic kept the class' current stats.
The Hope class may reduce the crew slightly, but gain a bonus to it's turn rate.
The Horizon class may take a knock to it's hull strength, but give a better crew compliment.
If you choose to tailor your ship, then you perhaps just get the standard specs.
That, and as it has ALREADY been suggested, allow us to level up the consoles of our ships so we don't just have to fly a RA class ship to use the full potential of a BO.