Of all the customisation ssytems I have seen, Ghost Recon: Future Warrior get's my 10/10
(Watch from 2:30)
I think this 'form' of customisation is perfect. You can select your weapon from a visually represented list and then when you want it customised, you get an exploded view in 'Gunsmith'. You can switch out a massive variety of parts, (which apparently come in at over 20 million individual weapon combinations.
20 MILLION!!!)
I like the APB:R/Army of Two visual customisation for gear and vehicles. If we can achieve this with Hard Armour, Vehicles and Weapon skins, I will be really, really happy.
(Pity the guy isn't very talented or patient, he could have got much better results.)
Now, if we went to a terminal in a shop or a fixers datapad, we could look at this sort of menu screen. Either way, we could customise our gear this way in a virtual environment, (which could possibly be unique to the supplier based on their background, crisp and clean for corportes, flashy and glitchy for back alley fixers, that would be a nice twist on it,) and have the supplier do the work, for a fee, and pick up the equipment when the work is done, (or even get them to deliver it for a higher fee.)
Now I am not suggesting that every supplier should have this facility. Perhaps we should go to specialists for it. But I do want to be able to get the equipment to do it myself, in my safehouse, when I have the means.
The customisation options should also change depending on what resources that are available to us, either from the supplier or from ourselves. The work should also take a variable amount of time, dependant on what needs to be done and wether the resources are on hand or if they have to be procured. I don't like instant upgrading. I think it was a big let down in games like Skyrim where I can apparently make a full suit of armour in under a second.