Thanks for mentioning Wordcycler! (I'm the developer.)
Older versions of Wordcycler did have problems with Instapaper rate-limiting downloads, but that's no longer a problem more recent versions, since Wordcycler now downloads content directly from the original article source.
There is however a hard-coded download limit of 400 articles per folder (increased from 200 in the previous version).
Wordcycler should work great if you don't mind syncing, reading a few (hundred) articles and syncing again. I would think that 400 articles would provide plenty of reading for the commute
If you have trouble getting Wordcycler 1.4 to sync more than 400 items at once, let me know.