Well, being from 'out west', I'm still pouting about the acquisition of Canadian Airlines by AC (though it's long past time to 'get over it'!)
I don't think you have to worry too much, just yet, about AC's financial troubles. . . transportation is too important to the government for that. If worse comes to worst, we, the taxpayers, will be bailing them out.
But you might find that the number of flights and variety of destinations changes. I wouldn't worry too much about losing popular flights like the one to Orlando. But what might happen is fewer seat sales to the popular spots as AC fights with the bread and butter business from domestic airlines like Westjet.
What I'm paying more attention to is AC selling a large stake in Aeroplan. Points tickets for popular spots were already hard to come by, and I suspect they 'may' get harder. Just MHO, I'm not an expert.
I'm also envious of the option of being so close to Buffalo you can fly from there -- it's getting pretty expensive to go south from here!
Anyway, the big difference between charters like AT, and regular carriers like AC, is the selection and regularity of flights, the variety of destinations, the baggage and seat selection options, regular check-in procedures and the seating space that the regular carriers provide.