Vine Whip is much slower to come out (frame 22 as compared to U-Tilt's frame 9) and covers a different area. Shorthop U-Air is also much slower to come out (5-frame jump startup + 12 frame U-Air), and the landing lag is definitely longer than the cooldown on U-Tilt, so those two are not always reliable options, especially against a character who can change direction on a dime, like Wario.
U-Tilt also has the advantage of completely moving Ivysaur's hurtbox off the ground, so while it isn't very safe to rely on the property, you can dodge attacks by doing it, especially if people were expecting to punish, say, a grab.
The two moves you described have a place in the matchup, but I think that relying on them to deal with Wario's spacing will get you grabbed too easily. In my head, U-Tilt should allow Ivysaur a faster anti-air to make Wario have to think twice before jumping in and grabbing her. Goes well with Vine Whip and pivot grab, for sure.