I would have no problem with "thanks in advance" at the end of an email sent to me. I would interpret that remark to mean that the person is thankful for whatever assistance I'm able to provide.
That said, I can understand why some might find this phrasing off-putting. If you think about it long enough, you can find all sorts of presumptuous or impolite overtones:
I already know you're going to fulfill my request, so I'll just thank you now.
I'm too lazy to write a follow-on note of thanks, so I'll just roll my request and my thanks into one message.
I wouldn't think you have anything better to do with your time than help me, so thanks for helping me.
However, I would be shocked to learn that anyone who wrote "Thanks in advance" at the end of an email really meant any of those things. That would be more a case of me reading too much into a commonly-used expression, I think, rather than a sender trying to be anything but polite.
That said, to answer your request for an alternative phrasing that won't be misconstrued, I think you can always go with something simple and plain:
That's succint but polite; it can mean as little as "Thank you for reading this," or as much as "Thanks for whatever support you are able to provide."
Many websites suggest closing a formal business letter with more specific words of thanks, followed by a more formal closing. In other words, you might see something like this:
Thank you very much for your time and assistance in this matter.
Thank you for considering these suggestions.
This depends very much on context, of course, but I find such formats a bit overly formal for some – though not necessarily all – email correspondence, which is why a simple "Thank you," can work nicely.
I guess I haven't added much more than ctype.h has suggested, although I think it's worth pointing out that a simply "Thank you," by itself is flexible enough to cover both of the meanings you are trying to preserve. If "Thank you," seems to common and trite, though, Wikipedia offers this alternative in one of its samples: