The problem is that the current implementation of MC isn't very modder friendly, the ONLY saving grace is how (relatively) easy it is to decompile java. What Mojang really needs to do is incorporate an 'official' modding API and mod-loading functionality.
In a perfect world, Modloader and Minecraft forge shouldn't be necessary. Putting in Modloader, ModloaderMP, Minecraft Forge, etc into the Minecraft.jar is too cumbersome for your average gamer to do, and the block ID problems mixed in makes modding really intimidating and hard to jump into as a newbie. Not to mention the pain that new versions of Minecraft bring, among other pitfalls. I can't tell you how many messages I get on Youtube from people who can't figure out how to install these mods. Granted, its not rocket science, but its more challenging than it could be.
If Mojang made modding easier on both the devs and the players, I feel like these mods would become infinitely more popular. If you could add a Minecraft Mod into your game as easily as you can add a WoW addon (Obviously apples and oranges there), the modding community would explode :). I think at the VERY least modloader functionality should be standard.
Thats all just my opinion though.