The reason why they are still in the exchange is because the price is nuts and no one is willing to buy them at those prices. This is why I usually see the prices as the upper bound on what people will actually pay.
By the way, I now have a mag regulator and all my weapons are anti-proton based. My advanced escort is ready for a dps showdown. My next big goal is to save up and equip a Sovereign class (so I can switch between attacking in my Prometheus and tanking in a Sovereign). I wonder if I can arrange my bridge officers so they'll function equally well on both ships.
As for Boff arrangements, it's a little bit of work, but you can do it. My Boffs are general purpose, which means their abilities won't do amazing things, but they're very cross compatible. I switch between my Excelsior Retrofit (which I love dearly), my escort retrofit, and my shuttlecraft, which I like to take into sector battles and confuse the hell out of new players as they watch me take on 5 ships at once and survive.