Weighting resource collection by how long you've stood there: Very interesting! I hadn't thought of that. How would it weight buildings, which stand there the whole time? That logic for collection probability is already fairly complicated, but I'm interested in thinking about this suggestion more.
I agree that combat is lacklustre! I'm planning on reworking it (yet again!) but don't have a concrete plan yet. Your ideas here are interesting, but I've been very careful to try to keep everything as streamlined as I can and avoid introducing special cases, so I'll be hesitant to make building rules more complicated. I might prefer simplifications like always giving resources to buildings instead of heroes, or something like that.
Towns/cities attacking: Cool idea - I'll think about this, too.
Thanks so much for your feedback and suggestions! This is definitely what I need. If nothing else, then for motivation to keep making improvements. :)