Pathfinder is pretty clear about the ability to stack templates, as there are multiple published examples of such. At issue is that some templates would seem mutually exclusive if templates are applied consecutively; for example, both Skeleton and Skeletal Champion are "an acquired template that can be added to any corporeal creature (other than an undead) that has a skeletal system".
Would it be possible for a spell caster (or pair of spell casters) to impart both the Bloody variant or Burning variant Skeleton template and the Skeletal Champion template onto the same corpse to yield a Bloody Skeletal Champion? Mechanically, if allowed, simultaneity of animate dead and create undead (the spells used in creating these templates) could be achieved by readied actions or contingency spells — so that's not an issue. The issue is entirely that consecutive application would yield a creature of a type invalid for the second template.