I'm not convinced the True Way is solely responsible for Bacco's death. I think this will end up being a Federation inside job a la Babylon 5. I don't trust the new Pres at all and get a President Clark vibe. I really hope I'm wrong on that and it goes a different way.
I don't get that. Ishan was originally unsympathetic to the Cardassians, but that lack of sympathy was both explicable by his personal history with the Cardassians and eventually mitigated (removing the clauses on Cardassian military spending). There's no evidence in TMS of Ishan doing anything outrageous like setting up paramilitaries under his control or bombing rebellious colony worlds or anything like that.
The novels of Swallow and Mack do
seem to hint at things going awry in the Federation, but we don't know what these things are or the extent to which Ishan is involved.
The only negative i can really think of is how Worf was handled. I wish he had a few more lines. it seemed like he said maybe 5 words the entire book and was there to take up space.
The whole matter of the Klingons generally deserves development. The expansion of the Typhon Pact is explicable at least as much by fear of the Klingons--the main feeling driving Gorn and Kinshaya membership, apparently--as by fear of the Federation, while the idea of being in an alliance with the Klingons was strongly offputting to many Cardassians. There's obvious room for improvement, I think, in the behaviour of the Klingon Empire towards its neighbours: a less aggressive Klingon Empire wouldn't be nearly as polarizing.