Of course there are major concerns with the reliability of WR/CR but I don't know any way around using them. Any ideal ranking would also consider PLs and Cup Games but I don't know any way to do that which would be remotely practical.
I would think that, putting issues of practicality aside, an ideal solution would lessen the weight of CR and would instead weight teams' actual performance in league matches - for example, a team that's throwing matches in the league to stay deep into the Cup may be increasing their CR but is definitely not making the league tougher. Of course, there are also problems with match ratings as indicators of strength - between the rating inflation for OT games and the fact that secondary skills which are often differentiators of truly strong teams not being reflected correspondingly.