Sorry the colours aren't working out. One of the feature requests in exa's pipeline is the ability to customise the colours, so you could make everything use bold colours if it's too dark, or make more things the same colour if it's too garish. Would something like this make it usable?

Speaking about the point in general, though, I think that terminal programs have been in a chicken-and-egg situation for the last decade or so with ANSI colours. Because colours only get used sparingly, not all terminals have good-looking colour schemes by default, which means they often look ugly, which means they only get used sparingly. There shouldn't be any reason why a terminal program should ship with unreadable colours by default (I have been killed in NetHack before because the default 'blue' colour in PuTTY was so dark, I could barely see it), and terminal programs that output colour should be smart about it (disable colours by default when not to a terminal, to avoid problems with grep like the one you cite).