Tommy,
Since routing is more a function of the land, and may control rhythm and sequence of a round, I tend to think of theme in terms of either the backdrop and setting, i.e. mountain, prairie, parkland, etc., or of features. And, IMHO, there is too much tendency to repeat features endlessly in the same style to either create or be accepted as a theme, i.e., narrow fw of Medinah or Olympic, the big greens of RTJ or small greens of Harbor Town, etc.
Regarding tree clearing/planting one course that disappoints to a degree is Shadow Creek, in that they had the chance to plant whatever they wanted, and all holes seem to have similar width corridors and similar looks with those pines they imported, again, just MHO on a fabulous course. I might have considered 2-4 wide open holes for contrast, and it would still have the same course them, IMHO.
Sometimes, it only takes 2-4 examples of a feature to create a theme. One conscious way I try to create a theme, without being repetitive, is to replicate a feature 2-4 times, in slightly different ways. If it is chocolate drop mounds, then (maybe) 2 as fw hazards, left and right, and 2 as green hazards in various locations that make sense, as an example. I don't feel like I need those on say, 15 holes to make it a theme, although, I could see that theory vary quite a bit. Or maybe one around a tee complex somewhere, even though its not really an integral part of the design.
For example, I don't think a course needs 18 greens with vast swathes of fw height chipping areas to establish a theme, and when you do that every hole, it becomes monotonous. Depending on a lot of things, I tend to think 6, 9, or maybe up to 12 greens with that (vs all rough grass and a few bunkers) would be enough for a golfer to remember those features as a big part of the course.
Or as one landscape architecture professor once told me, continuity doesn't have to equal continuously. And, as TD noted, architect probably think in terms of making every hole different for variety and memorability. I think non designers are more prone to saying "that hole is so different than the others." Architects tend to say, "Well, that was kind of the point."