I have had decent results (resto druid) simming a much shorter fight than the defaults. Something around 120s has given me stat and gear recommendations close to what I find from other sources. With the resto druid spread healing rotation, the sim starts to really oom at around 100s or so, so 120 seems to give some mana limitation, but not 3 minutes of fumes healing that a 5 minute fight would give. I still replace the weights with my own for resto, but much less modification is needed, and trinket suggestions match my expectations more closely.
The question of when to use mana trinks is a personal one, but they are more powerful than their item level indicates (generally) if you can use the mana (and MW can almost always use more mana). Also, with suggestions based on mana-limited fight sims, haste will be of even lower value for MW, since a lot of haste's throughput comes at the expense of more mana consumption (as opposed to druid, where much more of our throughput comes from hots).