There is a wood filler on the market that is almost a well-kept secret. It is Timber-Mate. An Australian product that does what the other brands wish they could do. It is water soluable and keeps well. It takes stains very well, unlike other brands that don't. It does come in various shades as well. Slightly more expensive than most but a real project saver when needed. I wish I owned stock in the company because once you use it you will never go back to the 'other stuff'. Also a trick told to me by a gunsmith friend is to use Fiebings leather dye on wood instead of standard stains. Using that he can hide 'misteaks' better than with other methods.
