In the Fullness of Time
With the Balance File Editor, hopefully we can sort out one of the bigger problem areas with gems, which is that they act as gruesome pothole diggers into the pacing of the game to artificially extend the minimal content that's present. In short, gems should never touch building/production times, at least not until a proper balance has been attained that makes them an actual choice, and not an outright necessity as they are presently. Alternatively, even with a proper balance, it may be best that they are used in some other manner.

This should be how they are on mobile too, but that's a separate business model entirely, in which I don't think they should even come near the gameplay too much, and should primarily be used in relation to aesthetic customizations.

Nurturing a Civilization
In a similar respect to the above, but distinct enough to justify this section, gems should likewise never be associated with belief and whatever stickers may become, under the same conditions as above. However, here we can expand on how gems may be acquired instead of pure microtransactions, follower sacrifices, chests, or voyages.

The gem seams are, amusingly enough, a tiny crack in the ugly web gems have woven throughout the systems of the game and present a better way of handling gems. Not only in gem seams, but in their emergence through actual gameplay, and I don't mean poking around the landscape for chests or shaping safe paths for followers in voyages because they're apparently legally blind, deaf, and whatever the absence of a sense of smell is.

No, instead, giving a chance of uncovering gems as wheat is harvested, ore is mined, and as the land is sculpted, would improve the acquisition problem. Now the next problem becomes, what are they applied to? They could be applied to what they are now, but as noted, that's problematic when a foundational balance is completely lacking (plus it doesn't make much sense for resources like belief or stickers).

Instead gems would make more sense as a traditional currency for your civilization that can be used to buy resources from other tribes (i.e. wheat/ore only) or to convert them to your side through bribes, alongside investing in happiness-related items. Rather than bloat the game through the introduction of trade goods and possibly another settlement type, make a formalized currency out of gems instead of trade good bartering.

In approaching it from this direction, you better integrate gems into the actual game world, rather than making them feel like the tacked on microtransaction currency that they are in the mobile version and only barely aren't in the PC version.

Diversifying a Civilization
Now this is where it gets a little sketch(y/ier), as online games have shown, you can technically get away with a microtransaction currency/microDLC and a retail price (e.g. Guild Wars 2). What you can't get away with consistently, is a retail price, subscription fee, and microtransaction currency/microDLC on top of all that (e.g. The Old Republic, The Secret World, etc.). So where does that leave us? Godus could, since it doesn't have a sub fee, get away with the retail price and microtransactions/microDLC, but it would be an extremely careful balancing act.

If you integrate gems into the main game more and keep them a microtransaction currency you risk making it pay to win. However this is where you could cut out the middleman currency for PC users and allow them to purchase cosmetic/aesthetic customizations directly as DLC, without having to heavily redo anything but the balance in the game.

Wait, wait, wait, where does mobile come into play?
Yet I mentioned making gems integrated more even in the mobile version, didn't I? How do we cross that bridge? There are a few ways, you keep them as I stated, purely related to follower interactions and world interaction as in the PC version, but you might reduce the amount acquired while still presenting the possibility of practical progress without depending entirely on gems.

Now, initially I said I'd prefer to keep gems as far away from the gameplay as possible on both platforms, and as much as I stand by that, I think the best way to do this is to bring them closer into the game so that really, it's only the excess/surplus that's needed/required for aesthetic/cosmetic microtransactions/microDLC.

What do I mean by that? In the core game, you can earn enough gems to play enjoyably without ever needing to pay for a microtransaction/microDLC. Through ridiculous amounts of dedication, you might earn enough to bypass the need for paying real money, as some players in EVE do by making enough isk to convert into PLEX, in Guild Wars 2 by making enough gold to convert into gems, or in Wildstar by making enough gold for CREDD and so on. Yet at no point does it ever become or feel like an absolute necessity to enjoy the game.

If you don't want to modify gems in this way, then withdraw them from all areas they touch presently and replace them with trade goods and reduce them to simply being a microtransaction currency. You may then convert accrued trade goods into gems in the same way as the aforementioned games do with gold to gems/credd or isk to PLEX. However, that would arguably be more work, and the aforementioned suggestion may work slightly better. You could, to keep them separate, refer to those purchased as surplus gems and not allow them to be used in the game and stockpile (i.e. convert) gems as (i.e. to) surplus for use on microtransaction content.

TL;DR:

PC version gems:

• Better integrated into the game by chance acquisition through farming fields/mining pits/sculpting or selling of excess resources (i.e. wheat/ore) to other tribes.
  
• The same resources may also be bought from other tribes.
  
• Convert via gifts/bribes. Conversion via belief through trees/beautification would still be viable, but may take longer due to subtlety.
  
• Never connected to belief or stickers (or whatever stickers may become).
  
• Aesthetic/cosmetic content would be purchased directly and separately as microDLC packs, if 22cans decides to approach additional content from this angle.

Mobile version gems:
Possibility 1:
*Similar to above, better integrated into the game, but perhaps acquire less compared to PC to encourage their purchase.

Possibility 2:
*Allow stockpiling of gems to create a surplus gem supply to purchase microtransaction content, but the prices would be adjusted so that this took dedication to do without negatively impacting gameplay.
*Modify gem purchases to be related to purchasing surplus gems for use only on microtransaction content (i.e. aesthetic/cosmetic content only).

Possibility 3:
*Gut gems, replace with trade goods, make gems solely a premium currency for microtransactions/microDLC.
*However, make it possible to convert trade goods into gems if enough are accrued.