The cores on higher quality intercoolers are usually more efficient than eBay ones, which is a lot of what you're paying for. Whether that matters or not really depends on whether you care enough to spend the extra money. If you just need any old intercooler, an eBay piece will work fine. If you're trying to make a good quality setup, pay the extra money. Obviously if the rest of the turbo setup isn't really great quality, it probably doesn't make sense to get an expensive intercooler because you're not going to see the benefit.

I'm not going to say much about the end tank design because I've seen eBay intercoolers with nice end tanks and I've seen expensive intercoolers with crappy endtanks.