Nothing really "makes" them expensive. It just looks like some sellers feel like charging ridiculously inflated prices. But then, are there actually people out there who are willing to pay these prices??? Because we all vote with our wallets... and if you think these prices are unreasonable, then don't pay them.
If sellers are willing to charge massively inflated prices like this and you as a consumer find it unreasonable, then just walk away. Because when you agree to pay these prices then you're justifying them to the sellers, and encouraging them to maintain the prices at such a high level. If on the other hand nobody buys these toys at their inflated prices, then the seller will either continue to stubbornly sit on dead stock (which some dealers do), or they'll lower their prices in an effort to elicit sales.
If you already have all these toys as Hasbro versions, then I see even _less_ reason to pay extra for the Takara versions. I wonder when Metals toys suddenly got so inflated -- because I got Metals Megatron in 2005, some 6 years after it came out (it was at this time my Transmetal Megatron succumbed to Brown Plastic Syndrome and broke so I decided to replace it with the superior Takara version), and I think I only paid about $50 or so for it -- which was already an inflated aftermarket price (original RRP 2500JPY [$30], and I paid about $30-something for TM Megatron from Kmart). So I don't know what's happened between then and now that's caused a recent spike in the aftermarket price for Metals.
If you happen to be intending on travelling to Japan, or if you know any friends who are intending to go to Japan or already in Japan, you might want to consider asking them to try and find some Metals toys for you, because BW toys there really don't cost all that much. I picked up a loose in box BWN Dead End for about 400JPY ('bout five bucks)... off the top of my head I think that toy would've originally retailed for 700JPY ($8.50)... so I managed to get him for nearly half RRP. Heck, if you know any friends travelling anywhere around Asia (China, Hong Kong, Singapore etc.), see if they can scope out collectable toy stores for Beast Wars Metals stuff for you -- cos if they can find any there, I'm quite certain they'd be MUCH cheaper than what you're finding on eBay atm. After all, you're essentially looking at collecting the _same_ toys over again but with a different box and a tech specs card (how well can you read Japanese?); I know that I always recommend against paying inflated aftermarket prices, but in your case where you already have these toys, I strongly advise that you consider avoiding paying inflated prices!