You have flowers everywhere most likely because you are using a modloader mod that adds flowers.
I was just recommending a fix for when someone was having flower issues.
Since installing this mod I've seen 30x as many free for all battles then my entire time playing Alpha.
I went to the Nether and nothing has changed, pretty much unaffected by this mod. Although when I created a portal at the bottom of the Nether, I was still transported back to the World portal at ground level. Haven't messed with multiple portals yet to see what happens.
BTW just for fun, I dug straight down and since no bedrock was present, fell through the map and into a blue oblivion.
(Not a real suggestion, just a dream) A cool feature would be using the GUI API (options menu) to set parameters for biomes when a game is generating. Using a percentage or ratio to adjust the amount: (For example)