Wolverine's movie height doesn't bother me in the same context that his comic height doesn't bug me. In comics especially, his height doesn't seem to stay accurate and that typically depends on the artist. Other characters are listed at heights taller than Logan and yet in the comics he is still drawn taller than them. Height and size in comics is a flexible thing. Look at Joe Mad's drawings of Wolverine fitting perfectly in the cup of Colossus' hand.
His height is mostly in the context that someone mentioned before, it goes with the ferocity of the character and the animal he is named after and the fact that his height is often the butt of insults against him, most commonly called "Runt". Other than that, it really has no bearing IN MY OPINION on the character whether in the comics or in the movies. He still does superhuman actions regardless if he was 5'3" or over 6'.
Ultimate Wolverine is actually listed as 5'9" which is probably more accurate to how the 616 Wolvie is depicted despite being billed at 5'3".
It's not like Wolverine has ever been depicted trying to jump up and reach something on the top shelf either.
