Yeah - what you say here is spot on. I'm making a new, larger version of the game and spending a lot more time planning the areas and routes through them. With some clever level design I think I can avoid most of the annoying issues people are having. I'm also going to introduce some items which can help you out of tricky situations (like an item which will re-charge your battery and clear your input effects - it can be used as a 1up as well as effectively letting players skip difficult areas).
And yeah the battery is my mistake - it runs on empty for a while longer than it should. =/
Thanks so much for the review!