You can requests a seat reservation any time when you go to the terminal ticket counter - even on the train. The Cisalpino used those old trains with compartments that were stuffy. The newer trains on Eurostars are much better. If Cisalpino is really gone, that is good news.
I liked the compartment cars; they were very cozy. Cisalpino used both compartment cars/open cars pulled by a locomotive and new Italian tilting trains with open cars. The tilting cars often didn't work properly, and the Swiss finally decided they didn't want them on their tracks anymore. The Germans didn't like them either (Cisalpino also ran from Milan to Stuttgart with the tilting trains, and they were more often than not late.) The new Swiss/Italian services (I hear, I haven't seen them) are generally individual cars pulled by locomotives; but some new Italian tilting trains (electric multiple-units) are also to be used (starting when?). Whether these new tilting trains will work is an open question. The Eurostar trains operated on domestic services by Trenitalia (dual-frequency) seem to work much better than the tri-frequency trains that ran north of the Alps (which were not branded "Eurostar"), but the most modern ones are just updated versions of the Cisalpino tilting trains.
Yes, this is long-winded, but I hope no one thinks the post-Cisalpino trains will be anything flashy. If the cars are Swiss rather than Italian they will be comfortable, clean and very well-maintained. Be glad.