It might be useful to try and pick apart what exactly it is you want the shop to do in gameplay terms and then think about other ways of achieving the same goals through different (possibly multiple) means.
So, a shop typically fulfills some of these roles:
- Gives meaning to the concept of currency as a reward: i.e. it gives you a reason to want to collect money/credits/energy/whatever and potentially sets up some interesting risk vs. reward scenarios. Could be replaced with some other form of reward that aids progression in a similar way. If you wanted to simplify things you could just replace monetary rewards with experience point gains, since they basically fulfill a similar function in this regard.
- Allows the player to make strategic decisions about the way they want to play the game by letting them choose their equipment (within certain limits) rather than having to rely on whatever they can find. Could be emulated by having characters or containers that let you pick only one object out of a selection.
- Makes all items useful in some way, since even if you don't use them you can sell them to exchange them for something you do want. Of course the downside to this is that the player usually then feels compelled to pick up everything he can carry just so he can sell it and thus engage in lots of dull inventory management, so you may want to avoid this anyway... but, could be replaced with some kind of 'recycling' or crafting system where items can be broken down and used to build other items.
And probably a few more things based on the specific game - I'm sure you get the idea: rather than replacing the shop system with something that acts exactly the same way but that has a big sign on it saying 'this is not a shop, honest' you could break down the functions of a shop into separate, potentially more setting-appropriate, forms.
