Focusing on the balancing/gating elements might be helpful, right now 3 examples come to my mind:
PS:T has the Lady of Pain.The first time i played the game, i abused the respawning of certain NPCs with killing an Abishai in the Hive over and over again for easy and early 7k xp. Now the Lady of Pain could have interrupted the killing of her residents with "STOP THIS NONSENSE! FEEL MY SHADOW!" and this would have been totally acceptable. Or think about the Cowled Wizards in BG2 - if abusing the system requires you to use sorcery (maybe through wishes?), they are able to gate your silliness by protecting the null-magic-law.
Tactics Ogre has level scaling enemies :--/ and being overleveled gets you vastly decreased exp, same with Final Fantasy Tactics iirc. But the cool thing about this game is the huge number of medals (=one time stat increase) it provides, medals who are often way stronger than several lvl-ups. One of them needs you to do 5 times in a row a successful ranged attack, which feels neither stupid nor degenerate. And the introducing of a Training Ground/an Arena doesn't let you feel silly if you feel the need to maximize stat gains.
You could even compare Tactics Ogre's medals with the abilities in FF9 - many really strong abilities can't be get through exploiting the systems or grinding. To gain these abilities (=items) you need to dig (
) deep into the game and do side quests, minigames or use the well-designed crafting system. Of course there is always room for improvement: FF9 stat gains per lvl-up increase when you already have high stats so you can exploit that by a low-lvl run to collect the items with the most stat bonuses and do the lvl-ups after that. Hm. But since the game doesn't have lvl scaling, this behaviour actually provides a challenge.
3rd example would be X-Com. There are several silly exp-maxing strategies you probably all know but there is a maximum stat increase you can get.
Knights of Honor had the option to have real-time battles (worldmap-time doesn't stop in a battle) and since in this game fights could have been won without a single loss if you just took your time and sniped everyone this option encouraged you to fight more aggressively to prevent seeing your kingdom in ruins after a battle.
X-Com would totally work with such an option (1 turn = 1 hour maybe) to prevent further torturing of poor silacoids.