It is stupid when a suit has less slots because of some stats. Like the Amarr Assault suit for example. It has one less slot than all other assaults suits at all tiers, but that's "ok" because it has higher base HP. But essentially all that means is you have the same amount of slots as the other Assaults, but one of them is locked in as an HP module and you can't change it.

Give all suits of the same class the same number of slots. If giving a suit another slot creates an imbalance, then take away some of the base stats to make up for it.

No it doesn't. Note I am saying give all suits of the same class the same number of slots, not the same slot configuration. And there would still be differences among base values of the stats.

I said it before, and I'll say it again. Stop using slots as the bargaining chips for balance! Balance suits by changing the base stats, don't take away slots. And suits like scouts and commandos have far too few. Again, remove some base stats and add in slots (and appropriate CPU/PG to account for that). If players want those base stats back, fit the appropriate module and you're right back where it was originally. But if you don't, then you have the option to add a different module to make the suit more unique and specialized to you.