I think it's awesome that postgres allows you to code in different languages like this. It really is a unique development environment and one that is overlooked as a development platform. It would be nice if more languages were delivered in the default package especially lua, V8 and mruby.
It is about dependencies and maintenance. There are not too much people who has good experience with C embedding Lua, V8 and others. Any people who can do some work are welcome.
The living outside main package has disadvantages - only enthusiast knows about it, but some advantages too - you are not fixed on PostgreSQL development cycle, and development can be faster.
My recommendation. See them as tools in a toolkit, not a question of what is best.
For places where you have SQL statements as primary do SQL or PLPGSQL functions.
For places where you are manipulating values (parsing strings for example) use something else (I usually use pl/perl for string manipulation but ymmv).
PLPGSQL works best where you have a large query and some procedurally supporting logic. It becomes a lot less usable, performant, and maintainable the further you get away from that.
So there is no best just different tools in a toolkit.
