I'd like to see these players able to make and modify devices.
It seems unlikely that a Star Trek MMORPG will allow players to create new kinds of things. User-created content is just plain scary to most multiplayer game developers; the potential for abuse by a few jerks looms too large for the perceived development effort. There's also the question of how many of a game's likely subscribers would use this content. Finally, a decision to focus a game's design on conventional MMORPG gameplay would argue against implementing a feature as significant as user-created content.
Having said all this, I don't believe it should stop us from knocking around some ideas on the subject of user-generated content in the sense of creating and modifying the functionality of devices in a Star Trek MMORPG. If not in Star Trek Online, then someone, someday....
So: my ideas on this (which I've described at much greater and more painful length in Starship Operations in a Star Trek MMORPG) boil down to applying two simple design concepts broadly throughout the game:
1. Build every complex object out of components that can be disassembled.The practical effect of these two things would be to give both Engineers and Scientists (including Medical specialists) opportunities for real creativity.
2. Allow the basic functionality of every complex object to be modified by its programming.
Given the appropriate tools and skills, Engineers would be able to deconstruct complex objects, from hand phasers to warp cores to starships, then put them back together again in new ways (and with different components) that yield new or improved basic functions. (The requirement for having the right tools for the job is important, BTW. Even given all the parts, no Engineer -- not even Scotty -- should be able to build a transporter using only a screwdriver and a paperclip. Repair one, maybe, but not build one.)
Scientists, meanwhile, would be able to modify the functionality of complex devices by writing computer subroutines that apply various filters to the outputs (energy, matter, information) of the internal components of these objects. Examples of this would be writing a quick subroutine that applies a dynamic inversion matrix to the output of a compression rifle to make it more effective against an enemy's shields, or a sensor enhancement algorithm, or a medical steri-field that adapts to a newly encountered lifeform's biology.
Taken together, these two features -- components and programs -- would form the basis for crafting in ST:O. And basing crafting in Star Trek Online from the very start on user-created content would allow players to enjoy the experience of creative problem-solving that is so much a part of Star Trek. (This approach also fits with the notion of "orthogonality" in Star Trek devices, which just means that in Star Trek there are only a few kinds of devices, but most devices have many modes of operation.)
I should note that, to some degree, this "Engineers work with objects, Scientists work with programs" approach is an artificial distinction. That's a fair criticism. After all, engineers in Star Trek (especially the later Ops officers) often reprogrammed devices, and scientists built devices. (Think of Scotty programming the Jenolan's transporter to store his pattern for 70+ years, or Spock's attempt to construct a mnemonic memory device using "stone knives and bearskins.")
Still, in terms of gameplay in a MMORPG, this seems like a reasonable way to insure that both Engineers and Scientists have some kind of useful creative activity they can do without breaking too far away from what's been seen in Star Trek.
Between these two capabilities, I think exploring the Star Trek Online universe would become as interesting as it should be.