Parthenon is a construction site right now. Also air pollution in Athens is not so good for marble. Remove the cranes, cut heating oil tax, and we will talk about it ;-)
The museum is arranged with the intent to display the complete set of pieces, with blank space deliberately left for the missing items, so in terms of technical housing I don't think there's a problem (this was part of the political motivation for building the new museum, to have a credible facility for the sculptures to be returned to). The caryatids are currently arranged as a set of six, but with one spot empty, and the frieze is laid out as a full-sized display of the entire frieze, with the pieces that the museum possesses inserted into their correct place, and plaster casts used as placeholders for the missing parts.