I disagree that Arsenal have contributed more but it neither here nor there! (15 by Arsenal, 18.5 by Newcastle - from UEFA cup AND Champions League!)
The right teams (ie Chamions league winners and semi finalists) are always at the top of it so it can't favour UEFa cup'ers that much.
I don't think you fully understand how the points work, they are accumulated over the last 5 seasons. Arsenal have contributed more in that time than Man Utd & Chelsea nevermind Newcastle.
Also on the one occasion you qualified for the Champions League in the last 5 years you accumulated 15.52 points, in the next 3 years you played in the UEFA Cup you achieved 24, 27 & 22 so yes it does affect the ratings quite significantly outside the very top clubs who consistently go deep in the Champions League. The only reason UEFA Cuppers don't get to the very top of the rankings is because they either progress to the Champions League (eg Porto & Seville) or they fail to qualify for Europe at all (eg Newcastle, Parma, Espanyol).
Espanyol accumulated more points than any other club last season (35.27) & lost the UEFA Cup Final to Seville who were 2nd highest (31.27) while Milan won the Champions League but were only 5th highest points scorers with 27.93. The previous year Steua Bucharest were ranked 4th & Middlesborough 6th!
Do you still think the system is fair?
We went a lot further in the UEFA cup (& won more games) than we did in the Champions league (mainly due to the two league stage at that time).
I would imagine the system takes account of teams that do well in the UEFA progressing onto the Champions league. (which allows the table to look right)
The system is based on a 5 year period - so when you break it down and look at one year it can seem strange.
With the league formats in the competitions you may get annomalies for a team doing poorly but qualifying from their league and gaining less points than a team they go further than. But over 5 years it will even out.
The table looks right, so yes I do still think the system is fair.