Basically you're talking about offline or down-time training, kinda like in Eve online, except instead of skills, you gain 'XP' based on a timescale, yes?
First of all when considering game systems I try to follow the following rule; if a system or mechanic in question supports the game world then give it a try. If the system can't be linked to the world, and you're only planning on using it because you've seen it somewhere else... consider whether or not it actually contributes anything to the game.
I disagree, at least when it comes to the type of 'customization' you're referring too. It really depends on the type of game you're playing. If it's a competitive rollercoaster like WoW, then most people are going to pick some kind of optimal build within a specific role (tank, dps, etc), so you'll mostly see the same few archetypes running around. A sandbox RPG allows people to pick different kind of specialties (crafter, builder, combat focus, etc), though almost everyone will try to max the most 'useful' skills either way, given enough time. If you want players to build a unique character mechanics wise, you'll need to build a game with a game-world that supports and rewards creativity, and you have to give players these tools right from the start. It's not something you can do with mere systems, rules and formulas.
You can't force people to 'enjoy' your game world if they don't want too. If someone is only interested in the grind and advancing towards the end-game, and you won't let them get to that point by their own efforts, they simply won't play.
That's one problem, sure. But I think most people won't even bother to go that far. They make a character; find out that they can't advance by their own merit and will simply quit playing. Why bother making a character that they don't want to play for a month? By that time, they'll have forgotten about your game and are already playing something else.
If you want players to make unique characters and enjoy the setting and the writing of your game world, make this the focus of your game. Reward people for creative thinking and exploration instead of putting them in an even smaller box.