Tim,
As another person who hires others to work on the plane, I totally, completely and empatheticly understand your question.
I started reading the ICS Forum solely because I was having similar problems and questions. I've learned a lot by reading other owner's issues.
One of the things I had to learn was each shop/mechanic has their own skills and what they are best at doing. At an annual, the only thing that is required to be done is the inspection but because, the dissasembly is already done, frequently airworthiness repairs and ADs, optional repairs or improvements are made.
It is true that a battery box that was fine in 2010 can deteriorate enough that it has to be rebuilt or replaced in 2011. The shop should give you the options and the pricing to go with it. There is an upgraded box
http://www.aircraftspruce.com/catalog/elpages/pa-28.php and I've goen to the gel battery to hopefully eliminate the battery maintenance and acid spill problems.
It is also true that one mechanic may view the battery box as fine and the next year the next mechanic has a different opinion. There will also be variances based upon how much Comanche knowledge the shop has. In this aspect airplane maintenance is very different than car maintenance. The older Comanches get, the fewer mechanics have lots of experience on them. Thanks to ICS posting the tech manuals on the website, I've learned by checkbook a lot about the parts and maintenance. I have no desire to be a mechanic but after a few years, I've learned to ask smarter questions.
The shop should be able to give you ballpark estimates for any work they propose, if not, I personally would look for another shop. Perhaps because you spent so much the previous years, they thought you want to spend that much every year - if you look at it from a business perspective, the relationship and understanding of the client goals takes awhile to develop. I normally prepare a list of what I want done in addition to the annual inspection and ask for an estimate.
Hope this helps. To read about the last annual I had done, see this website at
http://www.comancheflyer.com/NS/index-flyersN.php February, 2011 issue page 28. I'd be interested in reading about your annuals in future issues.