I don't know if I'd go with real-time scaling, but what about something like how Devil Survivor worked?
In Devil Survivor, the game takes place over the span of 1 week. You're given a list of locations and which people are at which location. Each person you talk to or major event you see advances the in-game clock by 30 minutes. However, there are more events than there is time, and some events only last for so long. So, if you notice two people having a conversation somewhere and you want to try and get information from them, you'll want to do so immediately because once their conversation is done, they'll each go their separate ways. The main challenge is that the game has multiple endings, and many characters will die depending on what you do or don't do, so you have to pay attention to what's happening and piece things together.
However, since the game is a strategy RPG, you can do Free Battles against enemies and it doesn't take up time, allowing for any necessary grinding or learning skills. (Think Final Fantasy Blue Magic. You pick an enemy with the skill you want, pick which character will attempt to learn that skill, and you need that specific character to kill the specific enemy to learn the skill. However, all units can then equip said skill once it's learned.)
Similarly, how about a setup like this. Major story events move up the "clock" and slowly bump up enemy strength. However, you can wander around and explore as much as you want without the "clock" advancing. Instead of linear story events, you occasionally have multiple ways to do things. For instance, lets say the game is something like Final Fantasy where there are four elemental crystals. At one point, you can choose to personally guard either the Fire or Water crystal. Whichever one you protect results in a unique boss fight against the enemy sent to destroy that specific crystal. The one you did NOT protect gets destroyed, and it's power is absorbed by the monsters in the game. This means that protecting the Fire crystal will grant some amount of Water-elemental power to the game's enemies, and protecting the Water crystal would grant Fire on the enemies instead.
So, this would reasonably mean that your weapons would start to follow a type-based system where your overall arsenal will change in effectiveness depending on your choices. However, to really add replayability, alongside tweaking enemy stats, you could add in occasional enemies that attack with the element that was spread around. What if, instead of giving the player the Candle to uncover secrets by burning things, enemy attacks would do that instead. So, allowing Fire to spread means you could start trying to make enemies uncover secrets for you by tricking them into shooting suspicious things. Or, have Water attacks push you back via jets of water, so you can stand next to a pit and try and get enemies to hit you and shove you across to a new area that you wouldn't have been able to access had you allowed Fire to spread around the world instead.
If you want to keep the real-time aspect, then maybe have something like Rings that power up your weapons to negate the enemies' resistances temporarily (like 15 minutes or something), so you can buy something to give yourself a boost, but if you don't hurry, you might end up somewhere dangerous with an arsenal that's not appropriate to fight with and no way to easily brute force your way through.