The rules seem murky on this topic. It says that while infiltrating the fleet a Cylon player is treated as a human player in all respects, except for some exceptions stated on the Infiltration card. So I guess the question is, is a infiltrating sympathetic Cylon a revealed Cylon player? The rules seem to say that a revealed Cylon player loses his character sheet abilities. But can you be treated as a human player in almost all respects and still be a revealed Cylon player?

No, he can't.

The cylon leaders are only type of cylons that can use abilities from their character sheets.

I agree the rules are a bit unclear since this is a "variant" but no, Sympathetic Cylons cannot use their character abilities.

Whoa...hold on a second. I'm confused now.

By "sympathetic Cylon" do you mean:

1. a player who was turned into a Cylon because he drew the Cylon Sympathizer Loyalty card during the Sleeper phase?
2. a player who is playing a Cylon Leader character and has drawn a Loyalty card from the deck of Loyalty cards generally sympathetic towards humans?
3. a player who is playing a revealed Cylon character?

In the case of 2. there is no reason why the Cylon Leader shouldn't be able to use his character abilities. A Cylon Leader does not equal a revealed Cylon character. In case of 1. and 3. the character sheet is turned face down upon being revealed...therefore you don't get to use any of the character's abilities.