MMCPilot
See here
http://www.pprune.org/tech-log/32681...t-weights.html
WAT limits affect aircraft in all phases of flight, but in the sense you are referring to, not in the cruise phase (or are not known as such, at least).
WAT limits generally refer to the take off, climb and landing phases.
As far as the cruise is concerned, basically the weight/mass will determine the optimum and maximum cruise levels but the real best performance will be determined in addition by the environmental (temperature, weather and wind), regulatory (levels available for the direction of flight) and strategic (forward planning vs other traffic).
The tropopause itself is not a factor other than the temperature implications.
From a theoretical standpoint, the optimal flight would be allowed a block of altitudes in which to operate (as Concorde often was) and would drift up and down as weight, wind and temperature caried. From a practical standpoint this is only available in a few, low aircraft density situations.