Travel from Aero Island to Kalmar

For Copenhagen-Kalmar I would also choose the regional Öresundståg to avoid the transfer. They are meant for commuters but works for longer distances too even if they aren't as comfortable as the high-speed train. They have toilets but no bistro or similar so buy snacks and drinks at the station if needed. They can be crowded but it will generally be calmer the more north you go (also depends on where rush hour is). Only half of the seats are bookable and in general few people buy a seat reservation.
There is a seat map here: https://www.oresundstag.se/en/travel-information/before-the-trip/
A lot of non-bookable seats are between door 13 and 14.
If you still want a seat reservation oresundstag.se is the first choice to buy and SJ the second. Prices are the constant and not dynamic so as long as there are seats left you don't need to buy long in advance.
If you don't want a seat reservation they sell an unlimited number of tickets without seat reservation so no need to buy in advance. If you buy in advance from the sites above your ticket is still bound to the chosen departure even if you don't buy seat reservation. Skånetrafiken is one of the partners behind Öresundståg and they have ticket machines at Copenhagen central (close to the exit towards track 1/2) and also an app. The advantage is that they are a little cheaper, on top of that they have a group discount starting at 2 people. One ticket for 2 adults is 715 SEK. DSB likely sell tickets too, when going to Sweden they usually have a family offer for 2 adults+3 children which is cheaper than 2 adult tickets.
Usually they couple two train units (or even three in rush hours) but decouple all but one before Kalmar so choose the front unit in Copenhagen if the platform signs don't say otherwise.

I know you take the ferry from Aero to Svendborg, but then it looks
like there are two options - 1.) take train which connects in Odense
to Copenhagen Central Station OR 2.) get the bus at Svendborg and
travel on bus to Nyborg Station where one then connects to train to
Copenhagen.

Which option fits your travel plan best? Generally, trains offer more comfort than a bus (though Svendborg-Odense is a local line, so it's pretty basic) - and if traveling with a lot of luggage, this generally is easier on trains as well. If you want to get one of the discounted Orange or Orange Fri tickets, they are only valid for trains, not for buses. And I'd recommend getting your ticket directly from DSB if possible. Rome2Rio doesn't operate any trains - whereas DSB is the main train operator in Denmark, and cutting out the middle man is often a good idea if something doesn't go according to plan. DSB will also be able to sell you a ticket all the way from Svendborg to Kalmar on their international ticket page. Not sure if this will be cheaper though, but something to consider.

And I agree with the other poster about the Øresund train all the way from Copenhagen to Kalmar. Just be sure to stock up on food and beverages, as there are only few and limited catering options on Danish trains as well.

Depending on how well the schedules match, it might be better to change at Copenhagen airport instead of the central station. At least there used to be direct trains from Odense to the airport. And I agree that it would be easier to take the direct Öresundståg from Copenhagen to Kalmar.

But, whichever option you choose, Ærø to Kalmar is a long trip so make sure you bring some food and water.