It is a little-known fact that mushrooms planted near mud will grow slightly faster. Let's augment this further by making them grown even faster still depending on how dark it is where they are planted.

Prohibit growing (or even planting) jungle trees outside of the jungle.

Nether portals should be prohibited above ground, this means it should not be possible to activate a nether portal if any of its blocks are above a certain Y-level, this means that the top-most block of the portal must be below this Y-level limit.

Proposed Maximum Allowed Y-Level: 24

An exception should make it possible to have portals above this Y-level, the conditions involved should result in exceptional portals being uncommon or even rare so that most portals are deep below ground.

Two Suggestions to Discuss

1. Special Flint and Steel Jonathan Suggested - If a very special flint and steel is crafted, this can activate portals anywhere. Such a flint and steel should be quite rare and difficult to craft.
2. Special Obsidian Block Kevin Suggested - If a very special kind of obsidian block is crafted, this can be used to build portals that can be activated anywhere by normal flint and steel. Such obsidian blocks should be difficult to craft.