So this has been bugging me for a while now, even more so with the inconsistency that I see between WotC and 3PP, and Monster Manual III. Does no one seem to understand their own creations? I see templates without LA. I see templates with LA that are incredibly low CR but ridiculously high LA. I see monsters with LA and monsters without LA, despite them being low HD creatures of intelligence. Then you've got templates and creatures alike that a ridiculously high CR that couldn't hold their own against a single PC in a one-on-one battle let along four, and then you've got creatures with a stupid low CR that could wipe the floor with 10 PCs of that level. How can there be that much inconsistency?
Actually, monster books got quite better over the years. The basic MM is pretty hit or miss, MM II is horrendous, but MM III, IV and V have much better consistency.
So, my main question is this: a) What determines the proper CR of a monster or template? b) Ignoring Savage Species, how does one figure out the proper LA for a template that can be put onto a PC?
a) The biggest problem with CR is that a monster can be engaged in a series of different ways. A troll is quite fearsome in closed quarters, but if you catch him in the open and with terrain advantage, he goes down like as smuk because he's slow and doesn't have ranged options. A succubbus isn't that dangerous in direct combat, but has crazy potential for intrigue, manipulation and social problems. As snakeman830 pointed out, one thing is finishing off a tarrasque in the open plains, another is stopping him from razing down a city full of mundane people while minimizing casualities.
I guess the only real solution would be splitting Challenge Rating into different kinds. "Dungeon CR" for trolls and the ilk, "Social CR" for stuff like the succubbus, "Skirmisher CR" for high mobility monsters, and "Disaster CR" for monsters that can cause a lot of collateral damage before they go down like the Tarrasque.
b)Again, it depends widely on the situation. Some abilities are pretty cool for NPCs, but quite dangerous if put in the hand of a PC that has party support and whatnot. Most monsters are exected to live some 5 rounds, PCs are expected to last a lot longer.
Lastly, is there some kind of book for homebrewers that I'm not aware of that help determine all this?
DMG. Part of the DM's job is knowing what makes a proper challenge and what doesn't, which strongly depends on the party and situation.
Because really, challenging a wizard that likes to throw around fireballs whitout metamagic is a completely different story than challenging the incantrix shadowcraft mage loaded with metamagic rods.