Comparing B2B reputation system to C2C/B2C's reputation systems is like comparing partner's for marriage vs date/one-night-stand.
People who dwell in business should know that B2B reputation relies on many factors that could not be easily built overnight. Seasoned purchasers or corporate users will look for various tell tale signs in addition to word of mouth and their experience to asses B2B business reputation and trustworthiness.
In addition, B users normally assessing their potential partners reputation by ordering small quantities of items or projects to minimize potential loss against fraud.
Also there is another issue of ensuring the reputation system itself is trustworthy in the first place (e.g. not rigged or manipulated by spam). Eventually, like all numbers, rating systems are easy to be manipulated - though I am sure this issue could be minimized given enough time and efforts.
So instead of trying to come out with a perfect reputation system, why do not change the angle: make it easier for B users themselves to asses the reputation of the said business.
- user feedbacks like what Aliexpress/Alibaba have is a bare minimum.
- show some parameters that indicate business trustworthiness in one
place for easy assesment (e.g. what is the BBB rating, what is the
company registration, location, SSL certificates, modes of payment, accept escrow, etc)
Hopefully after several iterations you could find out which kind of indicators are more important to asses business reputation and translates it into some kind of KPI as suggested by @Alexey
Here is some example of how Alibaba deals with reputation issues normally associated with China's supplier http://masoo.en.alibaba.com/company_profile.html I am pretty sure no scoring system could match this kind of information.