Which charge analysis is recommended to use for transition metal containing complexes?
This always just depends on what features you want. Hirshfeld and NPA will give you results that are reasonably stable w.r.t. basis set expansion. CHELPG (or better yet Merz-Kollman, which is symmetrized) are designed to reproduce the electrostatic potential and often used in force fields. Mulliken charges can still be chemically useful in compact basis sets.