Interesting thread - I think it raises some questions about just how much one can customize before it essentially becomes 'putting more queens in the field'. I don't play 'to win' like this, but I nonetheless do customize certain things: It's just annoying not being able to build a troop transport early and it seems too stupid and boring to settle for the default tax rates (which all the AIs are forced to use and thus suffer, making you gain the upper hand!).
The real issue, of course, is that things are done non-optimally in the first place - it's just weird that things get designed wrong by default. The underlying issue, however, is that a rebalancing is needed in many fields. This would also let the player just play the game without having to worry about nonsensical and tedious 'optimization' - and it would make the AI a lot more competitive, too! What's needed is things like:
1) Setting tax rate to just a few percent shouldn't completely destroy population growth compared to running 0% tax, it makes no sense at all. Honestly, the way it works is just bad; completely unintutive. I also doubt anybody truly enjoys managing tax rates but the game essentially forces you to because the penalty for not running 0% is so blatantly unbalanced.
2) Research model needs to change, it doesn't make sense that the optimal is having just three massive research stations. Of course one can conduct better research by performing it across many different locations and investigating different neutron stars/black holes/etc.
3) Place some limits on the amount of extractors, cargo bays, docking bays and more on a design by limiting their efficiency past a certain amount. Optimal play should be using designs as they are now so that one can't simply build ultimate editions of anything.
4) No re-designing of private ships to outfit them with sensors or other nonsense exploits (I actually thought this was no longer possible).
Basically, instead of making it optimal for the player to abuse the game rules, change the rules so that there's no benefit to be had from exploits. (Not to hammer on your post, Harrs, rather the game ;) )