My experience is the opposite. I work on a parsing/generation system that was developed in our group. Such a system consists of mundane parts (rewriting trees, applying a log-linear model) and sophisticated parts (parser, generator, guidance, grammar recompilation), and I find both to be natural in Prolog.

I suspect that you have just used the wrong tool for the job. Prolog works well for problems that require reasoning, and unification extensively. But if you are trying to write, say, a parameter estimator in Prolog, you are using the wrong tool for the job.