| Here's the thing: Either you care about exp or you don't.|
Either you're content to do whatever is it your character wants to do (I need to use the Ways to get somewhere? Let's go. Oh? I got exp on the way? Sweet!), or you're going to shape your actions around maximizing exp. Whatever system we put in place, if you care about the exp (and most people do) you're going to adapt your actions to produce the best exp return, regardless of how fun or convenient they are. That's just how gamer psychology works.
When you get right down to it what you're asking for is a return to "short timer, small exp", just with bonus exp based on how long it's been since you last did the action. If you knew you could use the Ways now for 50% of the possible exp would you really use them now instead of wait another 6 minutes to pick up 10% more exp? And at that point why not wait a few more minutes? Every minute you wait is more exp after all (setting aside clear mindstates and whatnot).
But the problem you're trying to solve is the tension between your desire to maximize exp and your desire to not have exp shape your actions. As long as you know "waiting = more exp" you're going to want to wait, not because it's fun but because it's rewarding.
It seems to me that a better way to address your complaint would be to drastically extend the timer to such a degree it is no longer practical to wait it out. Would that have downsides? Of course. But it would solve the stated problem.
Another solution to it would be to randomize the timer to a large degree. That, again, makes it far less rewarding to wait for the timer to elapse because the timer is now hidden information. This creates an awkward tension between checking if your timer was short (To maximize exp gain) and waiting until the maximum possible timer has elapsed (To minimize time investment). You could resolve this by having a message when the timer ends, but that rather defeats the purpose of the exercise since the information is no longer hidden.
I'm sure the current system could be improved on, and I welcome the feedback, I'm just trying to show why the situation is more complex than it appears on the surface. The challenge is to try and make sure that the rewarding activities are also the fun activities, but that's far easier said than done.