A major part of Persona 3's gameplay revolves around deciding how you will spend your time. As I mentioned before, the flow of time is central to the story and gameplay of Persona 3, and the decisions on how you spend the limited time you have are very important. There are many different things you can do on any given day, as well as some things you must do, but you can only do a few things in any one day. At any given time you may have to choose between building up different Social Links, raising your social attributes, hanging out with a friend to build up a friendship, praying for good fortune, studying, getting rest, or various other things. The importance of these choices can not be understated, and much like with Harvest Moon, the emphasis on the choice of how to spend your time really adds a lot to the game.
One thing I particularly like about Persona 3's implementation of the idea is that you never have to worry about wasting time by walking around and exploring a little. The time you are managing is "scene time", not real time; you have to worry about wasting an Afternoon, not five minutes. I think this is an improvement over the system used by another game with a similar concept, Way of the Samurai 2, where time was broken up into sections, but each section had a limit based on the passage of real-time. With no dependance on real time (you can spend five hours in the "Dark Hour"), you can feel free to spend time taking care of minor errands and exploring the town without impacting more significant choices. At the same time, you can skip through a particular chunk of time very quickly.
Another good feature about time management in Persona 3 is that you have to make different choices depending on time of day and day of the week. After-School hours on the Weekdays usually give you the chance to build up Social Links, build up attributes, or pray at the temple. Evening hours give you a choice between going to Tartarus (which gives up the Late Night hour as well) or going to the mall to build up attributes. During the Late Night hour you can sleep or study. On Sundays and Holidays you have a large number of special choices for the valuable Daytime hour. Beyond this, every character has their own schedule of what they do during the week, this all has to be balanced with the need to go to Tartarus and recover from the fatigue of battle, there story scenes and special events come up reasonably often, so it is very difficult to even have a reliable schedule, so you have to deal with each day as it comes. The game simply won't let you sit back and stop thinking about how to manage time.
Of course, while I really do like the system Persona 3 uses, there are a few places that I think it could use some improvement. I guess I might as well just list them...
1) I don't like the way days pass by so briefly during exam weeks. For some reason, you can't do anything on an exam week other than take exams. I don't really see the need for completely removing all chance to do anything on those days, when exams already limit your ability to build up Social Links and go to Tartarus a week beforehand. It makes months with exams and months without exams far too different.
2) I think there is too much stuff that can only be done on Sunday. There are too many contradictory things that can only be done on a Sunday, and most of them limit your ability to wander around and see what is happening on Sundays, even though that is the day out of the week where wandering around is the most interesting. It would be better if you had more freedom to explore. Maybe it would help if you could explore a bit before going to meet a friend on a Sunday "date"?
3) There was not enough done to make Saturdays seem special. The characters are supposed to have more free time on Saturdays (since they don't have afternoon classes), but there are no special things you can do only on Saturdays. Maybe it should have been possible to hang out with friends on Saturdays like you could on Sundays.
4) The Online Game you can play on Sundays seems to take up an excessive amount of the day. It is the only choice in which you must give up the ability to do anything in the Evening and the Late Night hour (including any chance to save) in addition to a Daytime hour.
5) This is a minor issue, but it feels like there should have been some choices open to you in the Early Morning hour to match some of the choices available at Late Night hour. Maybe something like a choice to sleep in late or interact with the other characters living in the dorm.
These few complaints aside, the time management system in Persona 3 is really good. There are a lot of things you need to do each month of the game and only a limited amount of time to do them in. There is always a constant pressure to keep doing things, so the game never really hits a boring lull moment. The choices are interesting, and the game itself never artificially gets in the way of making your choices. Figuring out how to spend the day is a lot of fun.