I'll look at prices again, but I'm comfortable where the fleetpoint values are at.
Fictionally, the Federation is going through revolutionary changes to its ship design philosophies. First, you have old ships like the Dakota, Titan, and Toa. Then you have established ships like the Ares, Orion, and Vixen. Then you have new ships such as the Rickshaw, the Antares, etc. During the production of these recent ships, some ten to twenty years ago, the Federation began to break its isolationist tendencies and involve itself in galactic politics. Ship design was greatly influenced as it learned from both new allies and enemies. The Scourge infestation forced some of these "new doctrine" ships into immediate production and a series of prototypes, either in testing prior to the invasion or specifically designed to fight the Scourge, were added to the Federation combat ship registry.
The descriptions and lore dates need to be consolidated at this point, but the following is when major Federation events roughly take place:
The year is 2595
-1500 years ago, the United Republic sends thousands of colony ships on distant one way trips to a galaxy far away, seeding life in the fringe of known space
-1000 years ago, galactic war breaks out and the colonies are thrown into a dark age
-350 years ago, the Federation is established, uniting the colonies under one flag
-115 years ago, the Jardain First Contact War begins
-94 years ago, the Jardain retreat to their domain and the crippled Federation begins to rebuild, marking the beginning of the Jardain-Federation Cold War
-76 years ago, a worker strike begins on several planets belonging to the mega-conglomerate UniTech United over living conditions and wages, spreading to two nearby systems controlled by rival companies. The situation soon becomes a violent uprising coined by the media as the Miner Rebellion. Three years go by with the rebellion gaining force, at which time the Federation military steps in and quashes it in 2 months.
-25 years ago, the Federation ends its isolationist policies and involves itself in galactic politics
-1 year ago, the Scourge invades populated galactic space
Making older ships affordable and useful is important, but instead of seeing them gain additional weapon mounts, you'll see new ships join the fleet. I have fun discovering the most valuable ship, whether it be for combat, cargo hauling, etc. Ships like the Dakota and Orion are there to give the player options, not to be the ideal choices for their credits and fleet points.
Combat isn't the only factor attributing to a ship's cost; the lovable Dakota-class has four (albeit strangely arced) small mounts, shields, a good deal of armor and some hefty cargo space. Dakotas are odd, a bit slow and have a lot of personality (i.e. they're patched together like a farm pickup), but they've proven their worth and are tough little frigates that the Feds use for utility roles. In short, they cost what they do because they're decent and hold more cargo than any vanilla frigate; I wouldn't send them on a suicide mission against the Scourge. What's most surprising is that of all the Fed ships, the little-frigate-that-could Dakota gets the most love. Three people have mentioned how much they care for them--they must hit a Serenity vibe or something. If an offbeat crew of bandits were being chased by the Tri Tachyon, I suspect they'd be piloting a Dakota.