The obvious disadvantage to using an INN player is they USUALLY just aren't too good. An INN top fielding SS though, could be an asset vs a poor hitting SS who can't field and just missed being INN.

The not so obvious disadvantage to using an INN player in RT, is that if he goes on a tear and develops some great stats by the end of the year (or earlier), you may find you used up all his PA's while he was INN and once he is no longer INN, he may be OVERUSED OR WORNOUT for the rest of the season. If you have a guy you expect to do better, I'd be cautious about using him while he's INN or better yet, watch to see you only use him at about 90% usage level [you can calculate what it would have been based on his PA's, games played to date in RT and games played to date in MLB]. That way when he stops being INN, you will still be able to use him.

Other than that, an INN guy isn't worse than his stats [my opinion] and some INN pitchers actually do quite nicely. Look at their ROPS/LOPS walks/IP and HR/IP to get an idea of how they might perform. Not all INN pitchers (or position players) are equal, some are almost good and some are terrible.