If Web services have all these problems, should I use them for production-level systems?
Although Web services do have some issues to be resolved, many of the alternatives do as well. Each technology has strengths and weaknesses. Now that you know what they are for Web services, you can make an informed decision on whether to use them for your project or not. If you're building a system to be used by many other people, Web services are probably your best bet.
If I go with Web services, how can I minimize the impact of the changes to the standards?
The easiest way to reduce impact is to limit yourself to using only standards-based options from the toolkit that you choose. That way, when the standards bodies agree on a solution for, let's say, security, you can easily add it to your code once your tool vendor updates its tools. Otherwise, you might be locked into a proprietary solution that might not be supported at a later date.