I like factorization because it uses a simpler approach to solar arrays, as well as not cluttering everything with complicated crafting recipes and GUI use. And who doesn't love the crystal actually growing in the crystalizer?
I agree with you to the extent that it follows what (one was) is the minecraft principle of simple(ish) rules, and complex systems. In minecraft, there are some fairly standard recipes (for armor, for example), which hold true universally. Most of what you craft can be seen in the recipe (chest is a wood block with a hole for stuff, furnace is a stone block with hole for stuff, etc.). The number of GUIs in vanilla is quite small (crafting, smelting, enchanting, storing, from memory), while a lot of mods go for complex, multi-stage recipes which work on what the item "should be" rather than what it is. Something like the generator would appear to be an efficient furnace below a battery. Buildcraft engines would seem to be plates of varying density, pushed by super-charge pistons, separated by glass. The recipes don't reflect what the item is.
I'm aware that it's not always possible, particularly with the tiers of tech mods, to do this, but factorisation does it well. The big changes are done by assemblies of blocks, rather than by crafting. You build a set of reflectors to power a solar system, which can heat things, or move things. The heater needs to be places near to things to work properly.
The major point is that factorisation (and, to a lesser extent, RedPower) encompass the spirit of minecraft, which is that space is the deciding factor, and the bit that you are constantly vying for. If you want an efficient smelter setup in vanilla, it's possible, but you have to have a ton of furnaces.. You can have neat and organised storage, but you need to have somewhere to store the chests. A lot of the tech mods try to fit large things into smaller spaces at the cost of expensive recipes (the advanced/compact solars is a good example here), which minecraft says that, if you have something complex, you build it yourself.
This is also the reason that I quite like frames as a true multi-block structure. There are a few components, but you build it yourself to your own needs.
Also, I may be slightly inebriated, so feel free to ignore any/all of the above, particularly the typos.
In answer to the OP:
MJ: With the present solutions and compatability
EU: As an potential answer, if the mods were forced to develop for it
RP2: As an idealized answer, if you could ever convince Elo to make something like a useable API for that damn stuff.