Hi Chaos,
Sorry to hear about the troubles you're having there. It sounds like a general limitation of computing power, more than anything else. Nothing jumps out at me there as being overall immediately off, but the number of units in a battle has an exponential effect on computational requirements. Splitting that out to no longer be the case and also to work across any number of threads in a multithreaded environment has taken us two years and a ground-up rewrite of the code in order to handle.
This doesn't mean that the original game is unplayable by any stretch of the imagination, but it is likely that you've chosen a more taxing scenario than you previously had, or that you simply accepted the lag spikes before without thinking about it, but now notice it. It's hard to say for sure. It could also just be an edge case where the computational requirements are super extra high for some reason (there are many of those sorts of things). The code itself hasn't been touched since 2014, so I'm not expecting that a change on our end would have made a difference here.
Bear in mind that your current hardware might be something like 2x or 4x more powerful than your prior hardware, but when it comes to one of those situations where the game freezes, you could be seeing a spike in processing requirements that is, quite literally, 1000x or even more. Processing power being the square (or worse) of the number of units in battle is a giant hurdle we had to overcome, and in general something that had been a focus on an ongoing basis since 2009. By 2014 we had hit all the improvements we could without just starting over from scratch with an inherently nonlinear approach; when I first started coding this game in 2008, multicore processors weren't a thing yet, and multi-CPU machines were rare. And multithreading code was a lot less efficient in general. In the decade since then, the entire computing landscape has changed, hence us needing to start over fresh, given then new ecosystem for that, in 2016.
All of which is to say: I'd try a different setup of units, or lower unit counts, or in general try to have fewer units fighting one another on a single planet. Or beyond that, the lag spikes are just simply expected because the game has to process hundreds of millions of calculations in a short period of time and it can't proceed until it's done. The sequel fixes that issue as well, but holy cow it took us like half a year to figure out how to make that really work and that was with the freedom to start from scratch. It's not something we can back-port.
I wish I had better news on this front, but I figured that at least an explanation of what is happening and why might be helpful. It's just thinking REALLY hard during those moments, and the reason it's thinking so particularly hard is because it's having to have every unit consider every other unit in the system in question. It's not a rendering issue or anything like that, but more about autotargeting and AI and tractor beams and all those fun things that "just work" but have to happen synchronously in this particular game (as with most multiplayer-safe games of its era).
Best,
Chris