Ok, so here is the skinny;
The concept is to balance templates with NPC classes. We don't want players to lose HD progression because of templates. Mostly because this translates to someone not gaining a level until the party is level 3, 4, 5, or higher depending on the template. This, instead, follows the logic that they PCs can progress normally offsetting the template with low power NPC classes since these give HD.
Initial HD:
So when the character is created with a template allow them to take the template at level 1, even if it is a +19 template, but here is the catch, treat the HD from the NPC classes that are being used to offset the template as racial hit dice for the template. This means they take average, not full, on the first HD. So someone offset with commoner would start with 4-hp, expert/aristocrat would start with 5-hp.
First Heroic class level, treat at first class level. So this level gives full HP, as it is being considered the first level.
So a character with a +2 template with 2 levels in Aristocrat and one level in sorcerer would sit at 16 (5+5+6).
NPC classes that should not be used to offset Template levels:
Warrior: a pretty sweet class for characters that target AC or are melee oriented. They get 1 bab per level, and have a d10 HD. The only negative is that they don't get the special qualities of the Barbarian/Fighter/Paladin/Ranger for level 1, 2, or 3. At first I thought this wasn't such a big deal, but that is still an extra bab per level. The choices of NPC classes, and the fact that most templates give bonuses to strength or dex effectively makes this +2 or more to hit from taking a template. We don't want this, but instead want the template to shine above the class.
Adept: a nice idea but 2 levels in adept gives a familiar, which might prove to be too good for classes that don't get familiars, or if someone is playing an exotic sorcerer that isn't going to get the arcane bloodline. For instance if a barbarian takes 2 levels in adept to offset a sweet template then he effectively has a pet and spells for little cost besides one rage power at level 20. Not to mention being able to use all wands that use spells from the Adept Spell List which includes the big 3 (healing, spells that cure status effects, and resurrection [Raise dead.])
Commoner: The weakest of all the NPC classes. This is almost a punishment IMO because while templates are nice they are often not as good as class levels. Later on many templates become worthless, or just a hindrance. All low saves, 1/2 bab, horrible skills, this is about as bare bones HD as you can get. In fact this progression is worse than every type of monster in the game, or at the very least worse than most of them.
NPC classes that should be used to offset Template levels:
For +1 and +2 templates the following classes offer exactly the same bonus to BAB (+0 and +1), but CR 3 and beyond templates favor the Expert and Aristocrat since these have 3/4 BAB.
(Fabliaux/Tragedy)Expert: This is a skilled character. If the character's backstory has him of low birth then go with Expert. Remember, these guys grow into heroes--or "adventurers" if you like your tales cynical--so they should at least have a decent save as well as 3/4 bab.
The catch with the Expert is that it is allowed to take "any 10 skills" as class skills, meaning it can be hand tailored to be exactly what the player wants. This isn't good or bad, it just means that the player is able to have a lot of wriggle room.
(Romance/Tragedy)Aristocrat: This is a noble character. If the character's backstory has him of high birth then go with Aristocrat. These guys, since they are becoming heroes--see adventurers above--they are probably going to have actual goals in mind. Where the Expert is more or less in an "common man" story the Aristocrat's story is probably more along the lines of a Romance--or Roman, going to the original meaning--where people of high standing embark on quests to achieve great things. As such these characters should at least have a decent save as well as 3/4 bab.
The Aristocrat is almost identical to the Expert, with the difference being preset skills--which he gets a lot of.-- Aristocrats have the knowledge of the wizard and the skills if a non-sneaky bard.
Story differences:
A Fabliaux is a story that has a lot of low behavior. This usually has a lot of comedy--integral to the Fabliaux--where there is an extended joke going along. Perhaps a character can never get laid, but gets his wing-man laid, much to his annoyance, and leaves to go on an adventure to leave his failures behind.
A Romance is a story of characters of high standing embarking on things of some importance. Almost every tale about knights doing noble deeds is a Romance, and modern day romances--ugh . . . --focus on Courtly Love to some extent or another, but this is only a single facet of what can happen in a Romance. For the bounds of Pathfinder a character's initial storyline can lead him down a path for personal gain(neutral), or for the gain of everyone(good). Just remember: A Knight in Shining Armor is a stereotype who is too good for his own good, even noble characters can have major flaws.
For added fun add a Rash Promise to a character's backstory: This makes it so the character, on his honor--if he has any--must go to do something or disgrace his word. Typically, this alone can be a motivation to get things started.
Also remember that the characters of high standing in Romances do not always have to be good people, and that some of them, while of high standing, are horrible people.
A Tragedy is a story where someone of high standing--not not necessarily always of high standing--falls due to his own hubris (excessive pride or self-confidence.) Typically this can be a descent into darkness personal plot line, or just a story where the character eventually ends up losing everything. This said things should make sense, and the things the character is prideful about should, in all cases, be his first fall-back.
All of the 3 examples above work for any alignment of character. A Chaotic good elf could be in a romance, a lawful good paladin could be in a fabliaux, and anyone could be in a tragedy.
So, recap:
Avoid using Warrior(powerful), Adept(powerful), and commoner(weak) to offset template "levels".
Instead use Expert(low birth), and Aristocrat(High Birth) to offset template "levels".
Yes, the templated character will initially be more powerful than the other characters, however when the full class characters are progressing the templated characters are catching up. They essentially multiclassing into classes that don't help them in any way aside from unlocking the power of templates.
Reasonings of choices recapped:
Warrior has full bab and d10 hp. This makes him an optimal choice, and essentially is a fighter -1 feat. Big deal for the gain you get from a template.
Adept gets spells, and a familiar at level 2. The versatility gained if this is your ONLY spell-casting class is enormous as it unlocks the ability to use important spells.
Commoner is just so weak that it isn't even worth your time. The power gained by a template isn't so great that it completely offsets the power gained by full heroic class levels. The commoner is about as literal of just giving an extra HD as it gets at all poor saves and 1/2 bab. To put it bluntly the Commoner sucks. Use this ONLY if the template is ~too~ good for the character's direction. If someone is going to take a template that offers a great deal of powers then them taking levels in commoner is justified. The Grave Knight Template is an example of where Commoner would be a good idea. Skeletal Champion or Lycanthrope are both not good examples of where commoner should be chosen.
Expert is great for characters who are not from high birth, mostly because it also suggests that they are productive members of society or at least are able to survive without begging for hand-outs. Think middle class.
Aristocrat is great for the same reasons Expert is good, but is of high birth. Has more skills than the expert, but less skill ranks. Comes from the upper class, and is probably driven towards some goal.