MrAl,
Let me try: The primary voltage causes the primary current which has a magnetic field around it. This magnetic field is also expanding and collapsing and thus cutting the secondary. Thus an EMF is setup in the secondary to counter the change in the current induced in the secondary by this primary flux. Is this right?
If that is right, the secondary induced EMF is a result of changing current, so it will lead the current. Thus the Voltage in primary and secondary are in phase.
This is what I figured out. And regarding my previous comment, there is already a phase shifted current in the primary (The magnetizing current). In the event that the secondary is loaded, the current drawn in the primary is a result of the secondary current. So if my secondary draws a huge in-phase current due to a resistive load, then that will compensate the comparatively small magnetizing current in the primary to lend a Primary current that is nearly in phase with Primary V. In the event that the secondary is also having inductive components, then the ratio of R to Z in the load decides the secondary phase shift. Is this right as well?
Now as per the analysis, the secondary current drawn will reflect in the primary. Now here is where I hope I don't muddle things up! The Primary now draws more current because the secondary current distorts the flux linked by drawing the current. Thus net flux is nearly constant. The primary current's behavior (i.e. phase shift w.r.t Primary V) is influenced by load. So the inductive load will create an induced emf that lags behind secondary V. Since primary V and Secondary V are in phase, the lag with Primary V and Primary I is increased. Thereby this is also said to be drawing more reactive power.
Has everything adding up in my understanding?