Ben here, lead game designer on Annihilageddon 2.
This is a great question that we have thought about a lot and plan to answer but haven’t quite gotten to explore a ton just yet (Cory keeps me and the other goblins busy making cool shit so what can I say we don’t always get time right away for this kinda thing!) so I wish I had some great answers/ideas already!
Ultimately like Cory said, whatever floats your boat :). But sometimes it’s hard to know how to float your own boat so I’ll try to offer what little advice I have for anyone, currently.
I totally approve a lot of people like Magikarp1 and MattWaste’s good guidelines. Beyond that I would say while it can be fun to mostly shuffle all of it together, consider just wholesale removing cards as part of your curation process as well (and let us know how it goes!). Most of the synergies and card abilities “scale well” with any size main deck assuming the card types stay relatively proportionate, and others like Dragon Ballz or even cards that reference less populous card types like Locations may be more reliant on the total composition of the main deck. I would say you might have the best experience keeping a combined main deck about the same size as it is in either A1 or A2 as standalone experiences, or if anything a little bit bigger is probably ok too (but the bigger you go, the more you risk just the narrowest synergies being too hard to pull off–the extreme nacho bonus cards from A2 for example will struggle to combo with each other with a big main deck).
A1 is a bit more measured in its pacing, while A2 is a little more explosive to help people get to those bigger legends…but both main decks also have a lot in common, structurally. If you’re going to try to combine both but cut the main deck down, the other big point I would make is that certain types of cards might ideally want to remain in close balance to how they are in a regular main deck: Defenses, damaging attacks, destroy-card effects, and Power/draw effects are carefully balanced through iteration and you would be surprised how “off” the experience can be when there are too many defenses, too many attacks etc. Even a main deck with say, 4 to 8 extra defense cards can make it dramatically harder to get attacks through. So consider keeping these broader categories balanced as well!
Another fun thing to do might be to focus on combining cards in a way that generates new context (especially if you’ve already played a lot of A1 and A2 and are just looking to make the cards function in “newer” ways). For example, I love the cycle of 4 cost cards from A1 that let you return another specific card type to your hand (like Bossu Fishmonger), and it could be fun to combine those with A2’s Legend Stack since they can now powerfully regrow all of the specifically typed legends from A2! Similarly, Stabby Steve gets that much stabbier with the higher costs floating around! But a card like Solzar the Wizard Star is kind of “the same” regardless of the context of the cards around it.