One important thing to remember when using Virtues and Vices is considering how they affect the character. I like to consider the Willpower benefit as a rush, almost like a high. Indulging Vices is something the PCs should be able to do in any given scene so long as they can justify it, but it will probably have ramifications. Indulging Virtues are harder to justify, and I think it's important to make them cumulative. Here are some examples of what I mean:
Paul is a police officer with the Vice of Wrath. He returns to the station after getting his ass handed to him by a werewolf where he used most of his Willpower. He yells at several people who cross his path in an attempt to regain a point, but he hasn't really felt the rush of his Vice. He still has that rage bottled up inside. He gets to the forensics lab and he finds out a critical piece of information won't be available for six weeks and he responds by angrily sweeping his arm across a table, knocking over and destroying several pieces of lab equipment. Now he is facing reprimands from the lab technicians and his superiors for his outburst, but he has earned his point of Willpower.
Erika is a furious maniac with a heart of gold and the Virtue of Charity. The first session, she indulges her Virtue by serving an evening at a soup kitchen. The Storyteller gives her full Willpower for it, and so she tries again next week. This time, however, Erika doesn't feel the same rush from doing this good deed. It doesn't regain her WP this week, but she desperately needs it for an operation the next night. Rather than spending two hours serving dinner, she instead gives five hours helping various down-on-their-luck persons obtain job interviews and flesh out their resumes. Great, she has her WP. The next week, she has to find a new way to indulge it, so maybe she spends her month's allocation of Resources on supplies for a shelter. The next week, maybe she actually gives up her Resource dot on a homeless family (as in she is now financially supporting them through repeat donations, or with a stock portfolio, etc.), and soon she has nothing more to give. She has driven herself into the ground to get those WP fill-ups.
From this, you can see the intentions of the developers: Vices have consequences for indulging them and Virtues require a toll before you even know if it will work.
Prudence isn't just retreating from a fight gone bad, it's refusing a lucrative contract because of risks that might not even be apparent to most people. Charity isn't donating a few dollars to the Salvation army, it's sacrificing your comfort to give others the same. Faith isn't praying in a pew, it might be going up to a gangster brandishing a handgun and preaching of God's mercy. Fortitude isn't staying up late to work on a case, it's continuing to investigate when assassins' bullets have hit you twice now. Hope isn't blogging about a wonderful day, it's hacking into a database to erase debts. Justice is putting down a friend who has decided he is outside the law. Temperance is vetoing a bill to increase comfort levels in a city because you recognize it will put the city in debt, despite it being an unpopular position. Indulging a Virtue is putting yourself in the line of fire for your convictions, especially when doing so won't give you any benefits.
It is for these reasons why Virtues and Vices were implemented the way they are, because they promote fantastic roleplaying by rewarding the characters for taking chances on disadvantageous actions. Houseruling them away means your players have no reason other than RP to stick to who their characters are, which is not sufficient for many players.
TL;DR: Vices should have consequences for their use (Morality is an excellent motivating factor), and Vices require characters risk their well-being in some fashion.