Thoughts cross my mind that I am seeing with Pathfinder some of the same explosion of content that was seen in DnD 3.x through its run.  Granted, I think that Pathfinder has done a pretty good job of keeping this increase in content from having the same direct power creep that we saw in its ancestor where new powers were inherently more powerful than earlier version, leaving older material less valuable, and older classes less functional.

That said, each piece seems to be relatively balanced vs. other individual pieces generally speaking, and they seem to have generally kept down some of the 'breaking' combinations that popped up otherwise.

However, I can't help be feel that one should keep in mind that Flexibility is wonderful... but it also has a subtle cost on the environment.  As an example, often the 'prestige' classes seemed a little power than the 'other classes' but one balancing factor was to be that it required skills or other abilities that would makes sense, but would not otherwise be 'optimal' to the average adventurer.

Or another way of looking at it, if you wanted to combine a particular race, to get its effect, but if by choosing that race you loose another benefit (by being able to choose a particular class as a preferred one) you have a cost for going that route.  If you for instance, create a sub-clan that makes this class an option... does that actually inflate the power of that race because now that 'perk' suddenly is no longer a cost of the choice.

Granted, I love flexibility, so I generally like the addition of flexibility, but I wanted to point out that this additional flexibility does have a cost on the environment, and does shift the power levels of classes and such.  For instance, everytime a new mage spell was published, the scope and potential ability of every wizard was increased.  When the first spell that allowed a mage to heal, it covered a former limitation of their ability, making their power grow.  There are just some thoughts in terms of campaign balance.

I don't want to 'say' stop this flexibility, but I do want to ask... what limitations should there be.  What ramifications for certain flexibility?  Should there be certain costs?  As an example, should there be limits to what spells a cleric has access to, not 'the whole' scope of all clerical spells.  Should mages have an upper limit of number of spells they could know, or have limits of non-core spells for instance?  Perhaps an exception being spells they themselves go through a full and expensive researching process?  Or is even that not really necessary?  Or do you give them a different cost?  Keeping a vast arsenal of spells known... costs a minus to their potency... dropping their effective level... or dropping their DCs of spells.  Or make spells past a certain 'number' become prohibited school spells... requiring two slots to cast.  I kind of like something like this as it doesn't outright upper limit someone from learning another, but allows a cost to further development in that direction.

Any thought on these ideas?

In 3ed and 3.5ed among the several published campaign areas there are very many spells.  For magic users (wizards &sorcers) if you wanted to make it possible for someone to use a variety of these spells from different campaigns.  I have thought that magic-user guilds/collages should have a limited number of school spells that are officially taught while advancing in level. The other spells known by the magic users are considered private spells either made by, found by, or awarded.
I would consider each guild/college to be a faction, which allows the member to pick school spells when awarded them for advancing in level.  I have no problem with them belonging to more then one school/faction but that would require dm agreement at start, or roleplaying becoming a member of the second. And possible paying an xp cost, as percent of level up.  Which might by spread over multiple levels

an example the entwort university of magic and the mind  has three magic-user collages lets call one Grayfalcon and the other Fyroon, each has the spell list for the campaign area they sound like.  Now we could say alright by law you could join two of the collages taking each as a faction gaining access to their different spell lists, but if you do this costs you two ability formation points from the pool you use to build your Characteristics.  I have been trying to recreate the level lowering method of creating Runts (zero level, members of more powerfull monstr races) and have thought of instead of lowering the ability scores directly lower the pool ofpoints to create those scores in the first place.  this actually might be usefull in more ways then one.  some say assimars are slightly over powered, so make the formation cost 2 or 3 point out of the pool.  like you I don't mind giving players the tools to create the characters they want.  add to this the idea that you can take a level lets call it a racial dice, and gain 6 of those points that would allow runts to grow to full strenth, AND allow could be used to allow a player to buy off overpowered prestige classes if not competely broken.

now also their maybe some items that I would only put in Certain backgrounds or Factions that had inate balancing issues.. you know DMs should have a table to roll for when a player has issues related to balancing "prices" end up in a given senario.