Your concern is one of the reasons I went to (lycra) cycling shorts. Deal with them when you stop for lunch, bathroom break, etc., and change out at the end of the ride. But you don't want more of that sales pitch. So ...
It's going to be difficult to get a good match for the crotch, not only in terms of flexibility and stretch, but especially in terms of color. Leather elbow patches on tweed elbow are fine on a professor's jacket, but they'd look pretty dorky on a crotch. Put them inside the trousers, and when you wear holes through then the reinforcement or patch material will shine through.
Iron-on patches sewed down at the edge work well for denim (jeans). For anything else, you might want to buy the trousers 4" longer than you need, then cut off the excess and hem or cuff what's left. The cut off part will match the rest of the trousers, and you can use that to double the crotch.