lol, I honestly don't think there is a solution to it other than typical rotations in the meta. As for banning Lotus targets, there really aren't that many that would need to be banned before Lotus decks were "ignorable". The problem is that there are a lot of Hyper-Versatile threats that Lotus can push out. You can still have strong Lotus decks that aren't 3 cards in 1. A few examples:
Inferno Titan isn't a great Titan because it's vulnerable to removal and still only attacks on one axis. It's power-level is acceptable as a Lotus target because a wider range of decks stop it.
Sorin Markov is an acceptable Planeswaker because he has no defence against creatures and is a slow-ish clock.
Dragonlord Dromoka is strong, but it's protection isn't universal.
I'll say it until my dying day: Lotus isn't the problem in this particular format (although it would be interesting to have a restricted list), it's the fact that 3CM is your typical Card Advantage game on Crack. Grave Titan is basically a 5 card 3CM deck...how can you compete with that? Ob Nixilis has an incredible amount of versatility, it can race alongside some of the most powerful decks, it can leap over the decks which stop creatures, and its a hard-to-remove type with built in protection: AKA: Superman.
Walkers are problematic for the same reason...by it's very nature a Walker is at least 2 cards in a 3CM game. The ban list would be easy to facilitate and easy to push Lotus out of unfair range...or at least easier than trying to keep Lotus banned by unbanning powerful enablers.
Edit: Oh, and for the Island argument, would you ban Island if this existed:
MegaIsland InstantIf you control two Islands, you win the game.
No, because plenty of cards work with Island and aren't broken. Island being able to cast MegaIsland isn't the problem. MegaIsland is the problem.
Edit2: Should MegaIsland's name be VintageIsland?