1) Probe Spam
I'm guessing the "issue" of probe spam would be fixed by their proposed priority list for each ship. I'd assume probes and trade ships would probably be placed at the bottom of every ship's priority list in that case.
I also don't think the the core issue of building certain types of (possibly) lower quality ships is much of an issue in an environment where each ship has defined, balanced priority lists. Depending on how priorities/ATKSPD/Initiative are implemented, it can make for more interesting strategic decisions as opposed to "just build as many of the biggest ship you have".
2) Planets, Planetkillers, Super-Capital Ships, and ATKSPD
Also to address the concern about ATKSPD = 1 ships. In my mind, Planetkillers are more of a specialized super-capital ship designed to one-shot other super-capital ships and (of course) kill planets. From that standpoint, having a huge ATK value but only ATKSPD of 1 makes sense.
For other super-capital ships, I think the previous poster's comment on them having more than 1 as ATKSPD has some merit. These ships (presumably) are built to take out the standard capital ship (Dreadnaught) as well as fight other super-capital ships effectively (and be less effective against medium-class, and even worse against fighters).
What I would suggest for these super-capital ships then is for them to have ATK value that is just enough to take out a Dreadnaught, but maybe ATKSPD of 5 and 10 (super-dread, monitor). So battle would play out like this (with some imaginary numbers):
A Super Dreadnaught (ATKSPD=5, ATK~=DEF of Dreadnaught) would take out either:
- 5 Dreadnaughts per round (most ideal target, basically almost all of ATK value used up on each ship, taking out the same number of ships as ATKSPD value)
- Some percentage of another super-capital-class ship (next ideal target, doesn't kill, but also doesn't waste much or any ATK value)
- 5 medium-class ships (not as ideal, perhaps half of the ATK value used up on each ship, only taking out 5)
- 5 fighters (worst case, lots of wasted ATK value on each fighter, still only taking out 5)
And you could use that similar model for all other ships in terms of balancing the numbers so that each class is most effective against the previous "tier"-class of ships (super-capital > capital > medium > fighters > super-capital)
Sorry for the lengthy post, but it's very exciting to see you guys willing to make needed changes to existing systems. My one last suggestion would be that whatever is done, make sure there is a very detailed and written out manual on how combat (and any other game system for that matter) works