One option would be to install the new sub-panel physically somewhere between the main AC panel and some of the AC loads, and move those loads' breakers to the sub-panel. Lots of work, but you'd free up space for future breakers.
Of course, that would only be prudent if you could re-run some of the circuits without pulling new wire for the existing circuits. And if you don't overload your AC system - we can assume you did a sanity check to make sure the 30A load wouldn't overwhelm your AC system - for a 3.5kw genset, you won't be able to run much of anything else simultaneously - like charging
the batteries (although you could probably run the genset for the bulk phase, and then startup the watermaker once it's well into absorption?)