One aspect that I'm surprised isn't mentioned is Data's endeavor to become more human. I'm not discounting the other answers: it certainly is a plot device to have data acting and speaking to the computer and crew members like any everyone else and they certainly did attempt to explain (or at least hint at) the incompatibility of positronic and isolinear circuits.
However, Data certainly adopted a number of anachronisms for the sake of relishing in the human experience. He paints, learns to dance, tries to be a stand up comedian, sings, plays the violin, emulates sleep, learns to dream and accepts foreign hardware that, to any objective computing standard, is a resource sink and distraction at best and a malicious attacker at worse (the emotion chip from Lore).
In his own words:
TIMOTHY: You sound like you don't want to be an android.
DATA: I am an android. That will never change.
TIMOTHY: But if you could change, would you?
DATA: I have often wished to be human. I study people carefully in order to more closely approximate human behaviour.
Also, typing and speaking don't hold him back very much, as his fingers can fly over the keys at super human speeds when required. (I can't believe I can't find a clip of his fast typing.) Ditto for speaking to the computer.
This is obviously not on par with an optical connection, but for every day ships operations tasks it clearly suffices. Perhaps a better question is why they even have a crew on the ship; the ship's computer is capable enough to fly itself, if they put the engineers put a little more effort into it. Unmanned probes could probably explore a lot more efficiently and cheaply than the more limited Star fleet.