When applying to work at a company, take care to write your cover letter carefully. This is not the time to demonstrate your eloquence, it is the time to get them to give you a call. Unless, of course, you are applying for a position as a writer, in which case my statement makes no sense.
Your cover letter is an opportunity for you to make each application unique. You can talk about the company you are applying to work at and what you can do for them. You can show off some of the research you did when applying to the company. You can write about some of your soft skills, which may be difficult to present in your resume.
You should not, under any circumstances, write about anything that would give them cause to not want to hire you. It is too early for demands and negotiation. Leave that until the interview and later (in fact, don’t mention any demands or negotiations until you have an offer on the table). If you have an issue which is important to you, make note of it to yourself so that you can ask the interviewer about it later. For example, if working flexible hours is important, and you can’t find anything regarding company policy for this on their website, make a note to ask about that at the interview.
The person in HR who is looking at the cover letters and resumes will only spend a few seconds looking at your application. If they see something negative in the application, they will move you to the no thanks pile immediately. After all, in today’s economy, for the job you applied for, there are quite possibly hundreds or thousands of other applicants. Why would anyone waste their time with the guy who’s whining about the number of hours he wants to work?