I find custom unit design in any game annoying, and frankly just another thing to do that detracts from playing the normal game. I'm playing a strategy game, and find the detail too tedious. The game should make the best units automatically for both me and the AI. Then there's no imbalance. I like building a civilization from the ground up, researching technology, and building cities, and I'd prefer to do that rather than spend hours in the unit editor. Having to customize units to such detail was one of the few things I disliked about GalCiv.
Make unit customization a disable-able feature. If the AI can't do it, why should I be able to?
Agreed. I think the only strategy game I've played that had enjoyable unit customization (outside of RPGs, not strategy games) was Alpha Centauri...and even then I got tired of it. I wanted to shape the future of Planet, not decide the make-up of my latest Chaos Impact Rover.
EDIT: Master of Orion 2 was fun to design units for. I'd almost forgotten that one 
The wonder of the Elemental series is the potential to strategically participate in the unfolding story of a fantastic world. Player decisions should be focused to this end. Unit customization is not an important decision.
If unit customization is in, it should be reserved for champions. Run-o-the-mill units should lose the grand scale customization. Instead, implement equipment quality the same as training options; something like "re-purposed farm equipment", "battered military equipment", "standard issue military equipment", "exceptional military equipment". Pick a basic unit template, pick a training level, pick an equipment level, and keep the game play focused on shaping fantasy kingdoms/empires.
I know unit customization is in, but I can live without it. It definitely isn't a deal maker for me.