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.