U-Multirank, which has been developed by academics and funded by the Commission, intends to reflect institutional diversity. It aims not to produce a league table, but to allow students, policymakers, employers and universities to choose their own criteria to compare institutions.
The project's pilot gathered data on 109 European institutions and 50 from outside Europe, including what is billed to be the first global survey of student satisfaction.
Speakers at the project's final conference in Brussels on 9 June - which reported pilot results and concluded that the system was feasible - criticised existing world rankings.
Adam Tyson, head of the Commission's Higher Education Unit, told the conference that rankings "can affect the decisions of governments about where to place their funding (and) affect the decisions of students - particularly the best students - about where to study". Yet they give a "simplified picture" of performance based mainly on research capacity, he added.
Mr Tyson described U-Multirank as part of the Commission's policy to counter the "homogenisation of higher education", which he said was among "the most distressing (effects) of existing ranking systems, in that it pushes ... institutions towards a single model of a research-intensive university, because that is the way you climb the rankings".
U-Multirank is led by the Centre for Higher Education, a German think tank, and the Centre for Higher Education Policy Studies, a research institute at Dutch institution the University of Twente.
Frank Ziegele, director of the German centre, said existing rankings had spawned a "reputation race" of "institutions trying to establish themselves as these famous, world-class, research-excellent universities".
The emphasis on rankings produced a "virtuous circle" for research-intensive universities, which can attract more funding, but a "vicious circle" for others regarded as "second best".
The pilot used 71 indicators across five categories: teaching and learning; research; knowledge transfer; international orientation; and regional engagement. Results were anonymised and will not be made public.
Only four British institutions - Newcastle, Glasgow, Coventry and Nottingham universities - took part.
U-Multirank's developers, who plan to roll out the project after a final report this summer, said that as well as European funding, they would seek public and private cash, including from possible media partners.
Conference delegates raised concerns about whether students would understand some of U-Multirank's technical fields, suggested that some users value the "simplicity" of an overall ranking, and questioned whether the project would cover a global spread of universities.