Which system for new character suits is more efficient?

I haven't messed with both options enough to be sure, but I think color replacing would technically lead to better performance? Then again, I don't know how that really works under the hood, so I could be mistaken. That being said, the performance different would likely be negligible on most modern computers, so unless your game can otherwise run on a low-end computer to begin with, or you're planning to port this to Android/iOS where that also might matter a bit more, I wouldn't worry too much. (Besides, while I could be remembering wrong, from what I recall color replace doesn't even work right on non-Windows platforms, so that might be worth keeping in mind too.)

Yeah, if you're making this for mobile devices you'll have to make multiple actives that are different colors. You can't use shaders or the replace color option. Multiple actives is also kind of nice because you can edit what each sprite looks like if you decide you want to go that route. Regardless of whether or not the sprites look different or if they're just palette swaps, when I use this option I typically have the player controlled character be an invisible object, then I just create the appropriate colored version and set its position to match the invisible object. By doing it that way you won't have a bunch of unnecessary invisible objects on screen.

If you're making this for PC and can use shaders, there's a color replacer shader that Looki made which can swap up to 9 colors in an image (and you could modify it to do more). Not sure how great performance would be with that though. It depends how many colors are in your image really. You could also use a shader to adjust the hue of the entire sprite, but you don't have any control over specific colors in that case.