"for larger nets, it doesn't necessarily make sense to print automatically all the infos about standard structural analysis (nodes without pre/post nodes, conflict sets, etc), or which places/transitions are not covered by invariants"
For this to implement it could be helpful if every message has an id. The id could be coupled to the analyzer and maybe some further information to toggle on/off specific messages, e.g., "InvariantAnalyzer.PInv.NumberOfPInv". Maybe it is also usefull to use either the logging system from java or log4j.
A message system, like described above, would only increase complexity. Therefore we stick to the old if-then filter mechanisms.