A major con is that it is slow for querying an SPK just to find its package name and description, because the whole package must be decompressed before the configuration file can be read. When comparing packaging schemes, it's fair to compare two things, the package file format and the packaging tools. As far as rpm and deb go, neither is a particuarly bad format. RPM is probably slightly more capable, with both of them having minor problems. In any case, designing a third incompatible format rather than fixing one of the existing two is the wrong answer.
Tools are slightly more of a Holy War.
Apt certainly seems to be the most popular, but rpm is much more capable for some situations. Not suprisingly, those situations also deliniate the typical users of the different distributions. As many people have pointed out, however, either tool could easily work with the other format, so writing new tools is also the wrong answer. The real issue is that Linux doesn't refer to a platform, or even an operating system, just an operating system kernel. So, enough's enough, adopt rpm as the lsb standard and get it over with.