In games highly dependent on time, I think they are a great addition, such as the Harvest Moon series where time management is a core gameplay aspect. In a linear story though it tends to muddy things up since time is generally abstract and the amount of time you spend on inventory, battle, or even wandering the field isn't necessarily indicative of how much time the character actually spent doing those activities and is usually easily brushed under the rug for the sake of story. It also allows for greater immersion to NOT have a time mechanic in certain stories where you can frame your narrative by means of time of day, certain events happening specifically at night for example.
If implemented in only situational places it can become a scrappy mechanic, while some may have enjoyed the time-based missions/battles in Final Fantasy VII, I found them unnecessary and a rather cheap way of adding tension or challenge.
So if your game is more laidback and less quest-driven then I think time-based gameplay works well, while I know some more modern RPGs use real time like The Elder Scrolls to rather great effect, there's a considerable difference in engine, and the RPGMaker Engine isn't really best suited to that style of gameplay.
I'm a big proponent of having your systems line up. If you have a turn based battle system which is based off planning and tactics for example, don't include Quick Time Events (QTE) in your game. If you have time move freely forward and responding AI packages to time of day, either incorporate that as a primary system similar to Harvest Moon or perhaps plan on having a mostly action based game.