Totally makes sense, thanks for giving specific examples, I can try to improve those. If you use the bug report form it makes it less likely that I'll forget about it.
A lot of it would be alleviated if the game would remember where the cursor was in a fight/dialog menu. This would allow, for example, spamming Starsight in the church, make the clock more useful, combat training less of a pain...
There should be a RPG Maker plugin for that, too.
Also, different actions should give different experience levels. Sure, I can train blacksmithing twice in the academy, or I can do it 60+ times at the blacksmith and get 30 times as much experience.
As you said, this is an RPGmaker limitation - I haven't seen a plugin for that specifically and I'm not sure if it's possible.
As for different actions giving different amounts of experience, they do! Taking a class in the academy spends more time and also gives you more experience than a single action of training it yourself that takes 1 unit of time. More differentiation will happen in future updates (e.g. new things you can craft but you have to learn at the academy)