Firaxis has laid out some plans for an upcoming update to Civilization: Beyond Earth, which (among other things) will be addressing the Wonders issue.
Apparently the Firaxis team keeps hearing that “certain Wonders were built only rarely, and players reported that some felt like marginal upgrades over other resource buildings,” so now they’re actually going to do something about it. In the next patch (which is being “prepared,” suggesting it’ll be out relatively soon,) Wonders will have their prices rejigged.
Wonder effects have also been changed on the majority of structures.
Civilization: Beyond Earth’s trade routes system is getting a revamp as well. Trade routes are said to still be “one of the primary resource generators for a given city” but will now unlocked through population. Construction of a trade depot gives a city one trade route slot, new slots unlock at unspecified population thresholds.
Firaxis intends this change to prevent players using small or medium cities as gigantic trade route hubs during the mid-late game. In addition, a player-requested “auto-renew route” option will be making its debut.
There are also various bug, AI and user interface tweaks and fixes listed in the official Civilization: Beyond Earth patch notes. You can see the specifics of the Wonder changes there, too.