So I had an idea that Major NPCs and even several minor NPCs would give you missions, with the maximum of 4 missions for each NPC. After a mission is completed, you'll gain a Mission Point and Trust with an NPC, which causes the NPC to recognise the main character more, as well as give comments and so on. I also had the idea that some missions would be timed, so that missions can actually be failed. They're not all timed, but events that would make sense for them to be timed are timed. I was also thinking that failing missions doesn't give you a game over, only affects a sub plot in some way.

Oh, I'm also suffering from writer's block

I think that's a great idea, but I just have one suggestion. Just knowing how I play games, very few players that are going to do "extra" missions are going to keep going if they fail one of them. If they're like me, they'll save right before they start the mission and try it again until they succeed. Writing extra branches for failed attempts is a lot of work for something that will probably not be seen, and if it IS seen it probably won't be appreciated by the player. I don't like being reminded of my failures lol.

If you really want branching sidequests from your side missions, you can always do the "Dragon Age" option (which I use too). Just add a moral choice at the end of the missions. Choosing one option will endear you to one character and anger another. The other option would do the opposite. That way you have lots of branches and complexity, but the path is actively decided by the player. That way the player feels like he has power, and not like he's being punished for how bad he played.

What do the mission points and trust points do? How do they practically effect the game?

I don't think having an actual time-counter for quests is a good idea because the player could be halfway through a quest and run out of time, and if that happened to me i'd just reset and try again or just not bother doing quests in the first place, but maybe "You have to do it before you get to point x in the game"....In Persona 4, gameplay is broken into calendar days but they don't progress through actual playtime, but the number of activities you do. For example, in a day you have the option of doing two or three of the following per day: shopping, visiting a dungeon, doing a quest, playing a mini-game, doing something to earn money, doing something to increase a specific stat, etc., and some things change depending on the time of the week/month (like the rewards for these tasks). Some of these options are only available on certain days of the week/month, so that gives the player incentive to talk to NCPs often. There is a time limit for each dungeon (you lose if you don't beat it by a certain day), but the player has the ultimate decision in when days progress. I hope that makes sense.