Re: Am I asking too much?
Maybe it would help get the job done more quickly & easily if you start smaller with cap needs to be replaced every time you use a marker (so before you go on to a new marker, the cap from the last one needs to be replaced). Once she is in that habit (and you may need to be on her to help her build it at first), then scooping them all up into a bin/pencil case isn't such a big deal when she wants to move on to something new. Plus, then even if she forgets, at least the good markers are getting dried out and you can simply put them away for the day/24hrs since they weren't taken care of.
A (usually) happy wife mama to my BOGO girls, DD1 July 2010 and DD2 Dec 2011.