I don't see it as a trade off today. In most models, at least the one's I've chosen, the designs are such that you can physically fit a larger displacement engine in the model than it was designed for without being too punitive on balancing issues, wing loading, all-up weight, etc...

I've never been faced with a situation where I had to make that choice. Pick an engine brand with a good track record and stick the powerplant into it that achieves the desired flying characteristics...