Water based are OK.. in all honesty every paint type has its advantages and disadvantages.
Water based or acrylics dry darker, so if you are colour matching then you need to make sure you colour match to the dried acrylic colour and not the wet.
Enamels are nice to use as you can colour match easily, but you can only do one colour a day as they take ages to dry.
My paint of choice is acrylic lacquer - dries VERY fast and retains its colour... in fact it dries too fast most of the time and so i use retarder thinners to keep it fluid for longer.
Whatever paint you use... bear in mind what sort of seal you are going to put over it - most CC's eat paint, so you need to make sure that your paint and CC are compatible.
If its an EM or SS game, then CC looks odd. For a perfectly safe and original look to the finish, i use polyurathane... its slightly yellowing same as original coating, goes on nice and then - same as original coating. But for an original finish and NOT high gloss, then a mix of 80% gloss and 20% low sheen gives a finish that has the same shine as original lacquer finish.
Hope this helps..
Gav