I have a question about the Merchant Guild. Does it pay 2 VP per EVERY production world of ALL four colors you have? Or does it pay out just 2 VP for a single one of each, maximum of 8 VP?

Because it seems like you could get a ton of VP's if you had a bunch of just 1 color production planets (like the rare element brown planets one of the starting card sets encourages you to try for).
And then what would be the point of all the other 6 cost developments that give VP's to a specific color resource planets, if Merchant Guild gave out VP's regardless of what number of what color production planets you had?

It pays out for every production world regardless of color. Note that this is production world, which doesn't include windfall worlds. The color specific 6 cost Developments give VPs for windfall worlds, as well as frequently having better special powers.

As for "Why the others:"

1) As Mark noted, the others pay out for windfall worlds. The Free Trade Association and Mining League have excellent consume powers, while the Pan Galactic League usually pays out as many, if not more, cards. All the others also pay out a bonus for one or two key developments.
2) Novelty Worlds are 9 production and 5 windfall. (64%) For other goods, the ratio falls. Rares are 46% production, Genes are 36%, Alien 25%. Overall, there are 21 cards that pay out for Merchant Guild ... that's a touch more than Free Trade Assocation.
3) Production Worlds cost almost half a card more (on average) than windfall worlds. Military Production Worlds defense averages one point higher. Production worlds cost more to get on the board -- they are slower. That's significant.

Which 6-Dev is good depends on the layout, but I personally find it easier to 'aim' for the Free Trade or Mining League (The Pan Galactic League or Alien Tech Institute take more planning/luck, since there are fewer matching cards, and those that do match are expensive ...)

Personally I consider Merchant League "OK." Sometimes excellent, it's frequently worth dropping in the endgame (for 6-ish points) unless you have a predominantly military or development strategy (there are only 4 production military worlds). However, SETI usually outscores it at 1 point per world (since there are 64 worlds and only 21 production worlds) and SETI has other scoring triggers (including 1 points for itself)

[Edit -- Cleaned up some sentences.]

I agree. At first glance it looks like San Juan's Guild Hall, but it doesn't work out that way in practice. The windfall exclusion is crucial, and makes it more interesting.

Thank you guys for the clarification. I guess that makes sense now that you've explained it.

The game's rules are quite well written for the amount of things going on and all the interactions you can get between the wildly varying cards. Thats been about the only question I've had that wasn't answered in the rules.