Probably not all investors took that sufficiently into account. Rating agencies do acknowledge the need to improve their rating methods for structured products. It may be worth considering a separate rating scale for these instruments in order to make it clear that the related risks are of a different kind than in the case of classic bonds.
One alternative could be to focus not on size but on the structure of the institutions and discourage complex structures. The problem I find with the metric used for measuring the systemiticity of financial institutions is that it is not an absolute metric but a relative metric. It calculates the systemiticity of a bank in relation to the global sum of various metrics.