Mine is Wario Land 4. And many people here on Wario Forums would agree with that.
It's just such a good game: the gameplay is awesome, the levels are gorgeous, the bosses are funny, and the game is not too hard (at least not on normal mode) nor too short, even though it has only eighteen stages. Plus the cutscenes are nice, and the music is really great and also worth to casually listen to. It's just as great as that of the more well-known Nintendo titles.
In short, Wario Land = best Wario game ever, and IMO also one of the best ever GBA games. If you haven't played it before, you definitely should. If you can't find a physical copy or don't have a GBA, try the e-shop of a more recent console. It's just too great to miss out on, and you won't regret playing it.
Yeah, I got a physical copy of WL4 about a week ago or so and I've had a lot of fun with it. So far I've beaten WL2 and WL3. The 3DS sadly doesn't have virtual console GBA games on the e-shop. (even though the 3DS would be able to handle it) The music isn't as good in WL4 as the previous 3 games, but the gameplay and some of the music is great. So far WL4 is definitely on the shorter side as you said, but the collectables and trying to 100% the game should help lengthen the game.