I honestly think the cap is fine. Put a mercenary space dock on control group 0, and tell it to not build if your total resources are below, say, 1,000,000 (in the ctrls-by-control-group menu). That way, you have 500k/500k at all times to refleet elsewhere.
Unfortunately, that's not quite how it works.
It means you have 1,000,000 M+C is reserve - not 500k/500k. In fact, since so few ships have even M/C costs, you usually end up with 999,999/1 as your 1,000,000 reserved resources.
I wish that it applied evenly to each resource... but this will stop being a concern when crystal goes away.
I'd love to see the ability to set the cutoffs for repair and construction be able to be set separately, or even just have one but not the other.
Yes, oh so very yes. I would like to be able to set these seperately as well, since I'd be setting the repair value to several times to construction value almost all the time. Instead I am forced to do manual repairing all over the place... boo.