First some comments on above:
2T10 Evocation - won't have any effect unless you actually have 2T10
Max Use Assumption - I would suggest checked, with this unchecked for example it will think it can stack all cooldowns even if they have different cooldown lengths without affecting their uptimes.
Sequence Reconstruction - For arcane it's ok to have this always enabled, it won't have any performance cost usually.
Some other suggestions:
Mirror Image/Flame Orb I would change to averaged, shouldn't have much impact on accuracy, but a large performance improvement.
Mana Neutral Cycle Mix should be enabled.
Hasted Evocation I would disable unless you're using advanced solver at higher settings (too slow to be practical), if you're using genetic solver it will support hasted evocation by default without affecting normal calculations in a negative way.
Arcane Light in general I would have enabled, disable this only if you want to examine effects of ramping up cycles into full burn or if you're using special fight conditions where it would be beneficial to use regen cycles (mini burns and similar), in general
if sequence reconstruction chart shows mana neutral cycle used not at full mana I would give this a try.
I've personally started using Simple Stacking mode enabled for normal optimizations. Mainly I've started doing this because of MWC+JC. Not that I think the normal solver necessarily overvalues that combo, it's more that the simple stacking undervalues it,
but I just didn't want to deal with 2 on use trinkets in practice to get the full value out of it.
As far as deep settings for optimizations go I don't have any good suggestions. For non-optimization I would definitely recommend the genetic solver, but that is mainly to solve optimum stacking solutions.