Teleport is only a problem if you allow it to be a problem. Traditional adventure design has progress foiled by physical obstacles that have to be overcome; rivers, chasms, walls, doors, and so on. Teleportation spells (including Dimension Door) circumvent all those obstacles. The common reaction to this is to make all important areas in the game world impossible to teleport into / out of.
I find that high level adventures are better foiled by information compartmentalisation. This makes sense in any organisation where the main form of advancement is stepping into the shoes of someone higher up on the chain of command (this should fit many organisations likely to be antagonists to your typical PCs), and the best way to ensure that people do not buff up, teleport into your room at night while you sleep and kill you is to make sure they don't know who or where you are.
If your adventure *needs* the villain to be in a specific location that the PCs can research well enough to teleport into, look into the Delay Teleport line of spells. When someone teleports into the villain's stronghold unannounced, their arrival is delayed for a few rounds. Use these rounds to summon some monsters and escape (via teleports for maximum irony), then clairvoyance into the room to get a tab on who teleported in, scry on them and Do Unto Others what They Did to You. This may seem like a cheesy counter-PC tactic, but it is a reasonable precaution anyone who has significant cause to worry about a violent death would take.
TL;DR: Don't nerf teleports to fit your preconception of an adventure, instead let teleports inspire you to make a new kind of adventure.