It pretty much comes down to basic economics.
The cost to make a mold for a typical 28mm human size figure I've heard is around $200-400. The cost to make an injection molded die for a plastic model is somewhere in the tens of thousands of dollars. When you amortize those investment costs into the cost of each individual model, the only way you can make it more affordable for plastic is to sell 100 times more than you would with pewter. Now I believe tooling for soft vinyl is cheaper than injection molding but you loose alot of detail and the parts are rather deformed and you pretty much get the crap that Wizkids and WotC dump out.
Models like plastic CAP Troopers and Arachnid Warriors come fairly cheap as each player needs LOTS of them. The Plasma and Tanker Bugs are much more expensive than what they appear (despite the lower cost materials, lower cost production facilities, and lower shipping weight than the pewter or resin alternatives) because the same investment costs (or more) went into making the molds, yet less are expected to sell (as you can only have something like a max 3 per bug player).
The only way Mongoose could justify plastic ships would be to make the game such that every player should have to buy the same models. Very difficult with as diverse of a collection at the B5 line has.
Anoither way is to market the game such that it could be sold to very large retailers in very mass quantities (like Walmart or Toys R Us). Of course it would be then dumbed down to a clix game and more than likely no longer supported by your FLGS. Another way is to force you to buy ships you don't want or need by randomly packing them.
Personally I'm glad that Mongoose picked up the old AoG molds and better yet are selling them for less than what the old AoG retailed them for. I don't know if you recall but the EA Poseidon Supercarrier from AoG cost $40 (and that was quite some time ago) and it didn't come with any fighters! I'd say that Mongoose is giving you quite a deal on pewter figures.
As for pre-painted, blech! I hate prepainted and find no added value in prepainted models (as I enjoy painting mine as much as I enjoy playing), especially if the paintjobs are crap.