I've been unsatisfied with how macrocannons outperform lances. So I've done an awful lot of calculations to try and find house rules that change the game in a favorable manner and make the choice of lance vs. macro interesting.
Here's what I've worked out:
Armour should count against each macrocannon hit, but armour should be reduced to account for the change. Specifically armour should be reduced by 12. That makes an armour 15 Raider have an armour of 3, an armour 17 Frigate gets an armour of 5, and an armour 20 Cruiser has an armour of 8.
The value 12 was chosen because the breakeven point between lances and macros with this rule is between 6 and 7. With an armour of 6, Dual Sunsears deal more damage than a Titanforge Lance and a Mars Macrocannon. Once armor reaches 7, the lance is more effective. By reducing armor by 12 that makes lances only worthwhile against the heaviest frigates, light cruisers, and cruisers.
It takes a little longer to figure damage, but it also makes armour work more like it does in personal combat.
Making this change to the rules does a few different things:
Armour is in general more effective when it gets up to high numbers. Raiders take a little bit more damage than the RAW, but cruisers, particularly with armoured prows, are nigh invulnerable to macrocannon fire.
The influence of Ballistic Skill on damage is reduced. This hardly means that BS doesn't matter; you still do more damage as your BS goes up, but the rate at which it increases is slower. This means that NPC ships can still do respectable damage and your Voidmaster won't blow up everything in a single volley. Say your ship is equipped with dual Mezoas and is firing on a frigate. If your BS is 50 the expected damage is virtually unchanged between these rules and the RAW (7.38 vs 7.52), but with a BS of 30 you deal twice as much damage as you deal with the RAW (2.48 vs 1.12). However, at BS 70 you deal less damage than you would with the RAW (12.56 vs 15.79)
High plus weapons like Ryzas and Pyros effectively become armour piercing, i.e. their relative effectiveness increases as armour increases.
Lances deal more damage against cruisers. This was the effect these house rules were intended to make and they achieve that without any other changes to how lances or macrocannons work.
Under this system a single cannon has a better chance to deal damage.
Mars Cannons aren't quite so bad.
Other things to consider:
If you change broadsides so that they inflict double the amount of hits (essentially giving them Storm), but reduce their strength to 3 (or 4 in the case of 1d10+1 Sunsears), they work better with this system. They are also much more capable in the hands on NPC ships without becoming too overwhelming in PC hands. They are downright frightening to lightly armoured ships though, but that seems acceptable.
Reducing the damage torpedoes deal by 12 makes them function identically under this system as they function in the RAW.
The effectiveness of bombers is subtly changed, and probably requires further examination. Their damage per hit may need to be reduced.
Reducing Sunsears to 1d10+1 makes them an interesting choice, rather than straight up better than Mars or Heculators. They deal more damage against lightly armoured opponents, but less against heavily armoured ones.
Since armour is more effective, bonuses to armour probably shouldn't stack. Adding Excess Void Armour, Armour Plating, and a Reinforced Prow together can make even lightly armoured craft extremely resistant to macro fire. Excess Void Armour may be too powerful all by itself.
Some alien races use variant rules that change effectiveness under this system. Rak'Gol macros probably need adjusting to deal enough damage. Eldar are even more fragile than they were and may need a small armour increase or some other change to compensate.