Create your own mod and do it yourself

If you just spent on more ships instead that would make a difference though, even if they hadn't got weapons upgrades..?

Also, though the mitigation dodge makes the phase missile upgrades more effective than the other weapons upgrades, at tier 3 there's also 20% hull upgrades.  At best the upgrade makes the weapons no better against hull upgraded ships compared to the initial state- but other weapons on the ships, not yet upgraded, will be less effective. 

Since the weapons have to be upgraded individually while the hull/armour/shields upgrades combine in their protective effect, the weapons must become gradually less effective...?

Later in the game, with a substantial fleet, the weapons upgrades become more necessary, when you've got the other upgrades.  If the incremental bonus was slightly larger for weapons, that might make for more of a choice earlier in the game.  Perhaps it isn't as much of an issue as the capship choice balance with the Marauder and Marza, but it might lead to greater variety of play. 

I still prefer to play the current version, rather than a slight mod.

spreadsheet that crap. do it. post it. 

seriously though, the upgrades are fine. maybe a little boring, but they work fine. 

one of the things that happens as fleet sizes scale up to a large size is that focus fire chains become more and more devastating. this is the reason why weapon damage does not need to upgrade on a 1:1 scale relative to defensive upgrades. its already an uphill battle for survivability just because of the natural effects of focus fire scaling in effectiveness with fleet size. 

If you want to spreadsheet it or graph it, you'll get a largely meaningless answer.  Even for more classical RTS mechanics that's an oversimplification. If you're just crunching numbers, then we can simply see how much a new frigate will add to the fleet's overall damage and health.  If we have 10 frigates currently, adding one more increases overall damage and health by 10%, clearly a better investment than upgrades.  There are many factors that make this inaccurate.

For one thing, consider this simple scenario:  10 units that deal 20 damage each and have 400 hit points, or 20 units that deal 10 damage each and have 200 hit points.  Clearly total damage and hit points are equal.  However, consider what happens after one volley of focus fire.  The group of stronger but fewer units has made their first kill, but the group of weaker units has only damaged one of the bigger units, not killed it outright.  Because the weaker units have lost some of their firepower, it will take two more volleys to make the first kill, and their damage output isadvantage will only snowball as the battle progresses.  In other words, fewer stronger units actually are better than many weaker units, even if the total health and damage output of both groups is equal. 

More recent generations of RTS games have more complicated features that also make the consideration less of a linear cost-benefit analysis.  A fully upgraded frigate and a completely unupgraded frigate both give the same amount of experience to a capital ship.  Clearly upgrading a unit will make the enemy have to work harder for each point of experience.  A smaller upgraded fleet may be weaker, but in the long-run their capital ships will be stronger because of it.  Another very obvious issue is upkeep; often times you simply cannot afford to acquire another fleet upgrade.  Generic damage and health upgrades give you an alternative to buff up your fleet without having to make that huge commitment to fleet upgrades.

There's even more to consider; special abilities from friendly capital ships and support cruisers may be enhanced by upgrades, while enemy abilities may be mitigated.  If you don't have health upgrades, you're just giving abilities like nano-disassemblers and flak barrage free reign.  On the other hand, every point of armour makes your hit points go farther, making Hoshiko healing (or any healing, for that matter) more effective.  Then you have upgrades like Vasari phase missiles which don't even fit in to traditional damage analysis because their effect is very situational.  Fairly useless if the enemy's shields are already down, but wickedly powerful if they're relying on Dunovs or Progens for healing.

I don't think there's an easy way to model this mathematically, and certainly doing a spreadsheet is rather pointless.  Sure, you can find where technically you get more damage by investing in an upgrade than you would from a new frigate, but how much does that tell you about what's going to happen in battle?

And even then, what does it actually mean to your strategy?  That's the real bane of statistics; the numbers don't lie, the problem is in the human interpretation of their meaning.  It's only helpful if we can say how those numbers impact a real fleet and battle, and that's more difficult than acquiring the numbers in the first place.

So weapons upgrades might be limited to allow more chance for capships to survive in the later game...?

I'm not sure that I follow the logic- there can also be some medium fire chains in the early game, when there are solitary capships at their lower levels and least hitpoints- why have capships vulnerable to a dozen frigates then, and not so much later...?

If phase missiles are the best upgrade, the wave cannons are possibly the worst, by the time you get the first one the upgrade is worth about 2.5% compared to the initial level of firepower effectiveness.

If the upgrades were doubled in effect, the protection upgrades would still have a considerable margin on them.  Another option might be to have more tiers for weapons research.  A third option might be to have the existing upgrades stack, so the 10% upgrade would be applied to the 105% level, then they would more nearly keep pace with the armour/hull/shields combination. 

Strategy... wave cannons make up more than half of the Marauder's weaponry, which explains much.  Why is it called 'Marauder' when it's the only interrupt-capable ship and has to be with the fleet?  As a lone plunderer it's useless, if it encounters a trade planet it has no ability to destroy structures or affect trade.  It's main raid ability only delays enemy warships being produced... which entails being in the same gravwell as the factory.  It can gate in a fleet, but this relies on enough of an infrastructure advantage that raiding is unlikely to be necessary, and this and the movement ability deplete its antimatter for interrupt.  If the fleet has to go back to defend urgently it can't even join them!

This may seem off-topic, but the inability of a lone capship to destroy structures as quickly later in the game is because its weapons have deteriorated compared to the strength of the structures.  Isn't part of the reason for longer fire chains poorer weapons?  With better weapons upgrades better firing micro might be more of a factor?

yes but you also have to consider bonuses to SBs and cap ships, which you can only have so much of.

upgrades are the only way to increase the abiliity of an SB to project power in its gravwell(except stars where you can build four).